StartDate: 2021-10-19 19:06:29+00:00 CpuId: 32x Intel Xeon W 2000 / D-2100 (Skylake / Cascade Lake) {Skylake}, 14nm CommitSHA: 4ac83d3d2bde3f6b60698d809a16c57cab54823e CommitTime: 2021-10-19 13:27:01 +0200 CommitAuthor: Matthias Krack CommitSubject: Accelerate test Trying to pull image cp2k-toolchain-mpich... success :-) Trying to pull image cp2k-gromacs... success :-) #################### Running Image cp2k-gromacs #################### ========== Fetching Git Commit ========== CommitSHA: 4ac83d3d2bde3f6b60698d809a16c57cab54823e CommitTime: 2021-10-19 13:27:01 +0200 CommitAuthor: Matthias Krack CommitSubject: Accelerate test ========== Running Test ========== Compiling libcp2k... done. ========== Building Gromacs ========== From https://gitlab.com/gromacs/gromacs 6e6e449b7..3590ab06f master -> origin/master * [new tag] 2019.3 -> 2019.3 * [new tag] release-1-6 -> release-1-6 * [new tag] release-1-6-01 -> release-1-6-01 * [new tag] release-2-0 -> release-2-0 * [new tag] release-2-0-01 -> release-2-0-01 * [new tag] release-2-0-02 -> release-2-0-02 * [new tag] release-3-0 -> release-3-0 * [new tag] release-3-1 -> release-3-1 * [new tag] release-3-2 -> release-3-2 * [new tag] v2016 -> v2016 * [new tag] v2016-beta1 -> v2016-beta1 * [new tag] v2016-beta2 -> v2016-beta2 * [new tag] v2016-rc1 -> v2016-rc1 * [new tag] v2016.1 -> v2016.1 * [new tag] v2016.2 -> v2016.2 * [new tag] v2016.3 -> v2016.3 * [new tag] v2016.4 -> v2016.4 * [new tag] v2016.5 -> v2016.5 * [new tag] v2018 -> v2018 * [new tag] v2018-beta1 -> v2018-beta1 * [new tag] v2018-beta2 -> v2018-beta2 * [new tag] v2018-beta3 -> v2018-beta3 * [new tag] v2018-rc1 -> v2018-rc1 * [new tag] v2018.1 -> v2018.1 * [new tag] v2018.2 -> v2018.2 * [new tag] v2018.3 -> v2018.3 * [new tag] v2018.4 -> v2018.4 * [new tag] v2018.5 -> v2018.5 * [new tag] v2018.6 -> v2018.6 * [new tag] v2018.7 -> v2018.7 * [new tag] v2019 -> v2019 * [new tag] v2019-beta1 -> v2019-beta1 * [new tag] v2019-beta2 -> v2019-beta2 * [new tag] v2019-beta3 -> v2019-beta3 * [new tag] v2019-rc1 -> v2019-rc1 * [new tag] v2019.1 -> v2019.1 * [new tag] v2019.2 -> v2019.2 * [new tag] v2019.3 -> v2019.3 * [new tag] v2019.4 -> v2019.4 * [new tag] v2019.5 -> v2019.5 * [new tag] v2019.6 -> v2019.6 * [new tag] v2020 -> v2020 * [new tag] v2020-beta1 -> v2020-beta1 * [new tag] v2020-beta2 -> v2020-beta2 * [new tag] v2020-beta3 -> v2020-beta3 * [new tag] v2020-rc1 -> v2020-rc1 * [new tag] v2020.1 -> v2020.1 * [new tag] v2020.2 -> v2020.2 * [new tag] v2020.3 -> v2020.3 * [new tag] v2020.4 -> v2020.4 * [new tag] v2020.5 -> v2020.5 * [new tag] v2020.6 -> v2020.6 * [new tag] v2021 -> v2021 * [new tag] v2021-beta1 -> v2021-beta1 * [new tag] v2021-beta2 -> v2021-beta2 * [new tag] v2021-beta3 -> v2021-beta3 * [new tag] v2021-rc1 -> v2021-rc1 * [new tag] v2021.1 -> v2021.1 * [new tag] v2021.2 -> v2021.2 * [new tag] v2021.3 -> v2021.3 * [new tag] v4.0.7 -> v4.0.7 * [new tag] v4.5 -> v4.5 * [new tag] v4.5-beta1 -> v4.5-beta1 * [new tag] v4.5-beta2 -> v4.5-beta2 * [new tag] v4.5-beta3 -> v4.5-beta3 * [new tag] v4.5-beta4 -> v4.5-beta4 * [new tag] v4.5.1 -> v4.5.1 * [new tag] v4.5.2 -> v4.5.2 * [new tag] v4.5.3 -> v4.5.3 * [new tag] v4.5.4 -> v4.5.4 * [new tag] v4.5.5 -> v4.5.5 * [new tag] v4.5.6 -> v4.5.6 * [new tag] v4.6 -> v4.6 * [new tag] v4.6-beta1 -> v4.6-beta1 * [new tag] v4.6-beta2 -> v4.6-beta2 * [new tag] v4.6-beta3 -> v4.6-beta3 * [new tag] v4.6.1 -> v4.6.1 * [new tag] v4.6.2 -> v4.6.2 * [new tag] v4.6.3 -> v4.6.3 * [new tag] v4.6.4 -> v4.6.4 * [new tag] v4.6.5 -> v4.6.5 * [new tag] v4.6.6 -> v4.6.6 * [new tag] v4.6.7 -> v4.6.7 * [new tag] v5.0 -> v5.0 * [new tag] v5.0-beta1 -> v5.0-beta1 * [new tag] v5.0-beta2 -> v5.0-beta2 * [new tag] v5.0-rc1 -> v5.0-rc1 * [new tag] v5.0.1 -> v5.0.1 * [new tag] v5.0.2 -> v5.0.2 * [new tag] v5.0.3 -> v5.0.3 * [new tag] v5.0.4 -> v5.0.4 * [new tag] v5.0.5 -> v5.0.5 * [new tag] v5.0.6 -> v5.0.6 * [new tag] v5.0.7 -> v5.0.7 * [new tag] v5.1 -> v5.1 * [new tag] v5.1-beta1 -> v5.1-beta1 * [new tag] v5.1-rc1 -> v5.1-rc1 * [new tag] v5.1.1 -> v5.1.1 * [new tag] v5.1.2 -> v5.1.2 * [new tag] v5.1.3 -> v5.1.3 * [new tag] v5.1.4 -> v5.1.4 * [new tag] v5.1.5 -> v5.1.5 Updating 6e6e449b7..3590ab06f Fast-forward admin/ci-scripts/build-and-test-py-gmxapi-0.3.sh | 12 +- admin/ci-scripts/gromacs-base-test.sh | 1 + admin/containers/scripted_gmx_docker_builds.py | 11 +- admin/gitlab-ci/documentation.gitlab-ci.yml | 8 - admin/gitlab-ci/lint.gitlab-ci.yml | 2 - api/nblib/tpr.cpp | 9 +- docs/gmxapi/userguide/install.rst | 4 +- docs/release-notes/2021/2021.4.rst | 34 + docs/release-notes/2021/major/portability.rst | 2 +- docs/release-notes/2022/major/performance.rst | 2 +- python_packaging/src/setup.py | 8 +- src/gromacs/essentialdynamics/edsam.cpp | 7 +- src/gromacs/ewald/pme.cpp | 14 + src/gromacs/ewald/pme.h | 13 +- src/gromacs/ewald/pme_gpu_internal.h | 2 +- src/gromacs/ewald/pme_solve_sycl.cpp | 11 +- src/gromacs/gpu_utils/sycl_kernel_utils.h | 4 +- src/gromacs/mdlib/groupcoord.cpp | 1 + src/gromacs/mdlib/vsite.cpp | 22 +- src/gromacs/mdrun/runner.cpp | 2 + src/gromacs/selection/evaluate.cpp | 3 +- src/gromacs/taskassignment/decidegpuusage.cpp | 23 +- src/gromacs/taskassignment/decidegpuusage.h | 4 + src/gromacs/trajectoryanalysis/tests/distance.cpp | 18 +- ...istanceModuleTest_HandlesSelectionFromGroup.xml | 2094 ++++++++++++++++++ ...ceModuleTest_HandlesSelectionFromLargeGroup.xml | 2270 ++++++++++++++++++++ src/gromacs/trajectoryanalysis/tests/simple.ndx | 37 + 27 files changed, 4559 insertions(+), 59 deletions(-) create mode 100644 src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml create mode 100644 src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml create mode 100644 src/gromacs/trajectoryanalysis/tests/simple.ndx Configuring Gromacs... done. Compiling Gromacs... done. :-) GROMACS - gmx, 2022-beta1-dev-20211019-3590ab06f (-: GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gaurav Garg Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx, version 2022-beta1-dev-20211019-3590ab06f Executable: /opt/gromacs/build/./bin/gmx Data prefix: /opt/gromacs (source tree) Working dir: /opt/gromacs/build Command line: gmx --version GROMACS version: 2022-beta1-dev-20211019-3590ab06f GIT SHA1 hash: 3590ab06f96f123de64973e14195db333cbc50ff Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX_512 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 GPU FFT library: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /opt/cp2k-toolchain/install/gcc-11.2.0/bin/gcc GNU 11.2.0 C compiler flags: -mavx512f -mfma -fno-omit-frame-pointer -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /opt/cp2k-toolchain/install/gcc-11.2.0/bin/g++ GNU 11.2.0 C++ compiler flags: -mavx512f -mfma -fno-omit-frame-pointer -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -fopenmp -O3 -DNDEBUG ========== Running Gromacs QM/MM unit test ========== [==========] Running 21 tests from 5 test suites. [----------] Global test environment set-up. [----------] 3 tests from QMMMInputGeneratorTest [ RUN ] QMMMInputGeneratorTest.CanConstruct [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) [----------] 7 tests from QMMMTopologyPreprocessorTest [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to -1073787013 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (6 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to -1076380193 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (5 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to -570690133 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (15 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 63.00 NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 129.093 K for determining the Verlet buffer size NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to 2140503805 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.013 nm Set rlist, assuming 4x4 atom pair-list, to 1.008 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (21 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 3 [file unknown]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 42.00 NOTE 4 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 193.640 K for determining the Verlet buffer size NOTE 5 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to 2071197629 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning all bonds into constraints... Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K Calculated rlist for 1x1 atom pair-list as 1.015 nm, buffer size 0.015 nm Set rlist, assuming 4x4 atom pair-list, to 1.009 nm, buffer size 0.009 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (14 ms) [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Number of degrees of freedom in T-Coupling group rest is 45.00 NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022-beta1-dev-20211019-3590ab06f (single precision) Setting the LD random seed to 1710681052 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (5 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (69 ms total) [----------] 9 tests from QMMMOptionsTest [ RUN ] QMMMOptionsTest.DefaultParameters [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) [ RUN ] QMMMOptionsTest.OptionSetsActive [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) [ RUN ] QMMMOptionsTest.CP2KInputProcessing [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) [----------] 9 tests from QMMMOptionsTest (1 ms total) [----------] 1 test from QMMMForceProviderTest [ RUN ] QMMMForceProviderTest.CanConstructOrNot [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) [----------] 1 test from QMMMForceProviderTest (0 ms total) [----------] 1 test from QMMMTest [ RUN ] QMMMTest.ForceProviderLackingInputThrows [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) [----------] 1 test from QMMMTest (0 ms total) [----------] Global test environment tear-down [==========] 21 tests from 5 test suites ran. (72 ms total) [ PASSED ] 21 tests. Summary: Gromacs commit 3590ab06f works fine. Status: OK EndDate: 2021-10-19 19:17:36+00:00