StartDate: 2022-01-24 11:02:22+00:00 CpuId: 32x Intel Xeon W 2000 / D-2100 (Skylake / Cascade Lake) {Skylake}, 14nm CommitSHA: 17efb48911a60e2c4c27ff53d9e1c09127373232 CommitTime: 2022-01-24 10:50:04 +0100 CommitAuthor: Eisuke Kawashima CommitSubject: Fix INTENT of calc_energy_func_der Trying to pull image cp2k-toolchain-mpich... success :-) Trying to pull image cp2k-gromacs... success :-) #################### Running Image cp2k-gromacs #################### ========== Fetching Git Commit ========== CommitSHA: 17efb48911a60e2c4c27ff53d9e1c09127373232 CommitTime: 2022-01-24 10:50:04 +0100 CommitAuthor: Eisuke Kawashima CommitSubject: Fix INTENT of calc_energy_func_der ========== Running Test ========== Compiling libcp2k... done. ========== Building Gromacs ========== Already up to date. Configuring Gromacs... done. Compiling Gromacs... done. :-) GROMACS - gmx, 2023-dev-20220118-fbf7230 (-: 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 Oliver Fleetwood 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 2023-dev-20220118-fbf7230 Executable: /opt/gromacs/build/./bin/gmx Data prefix: /opt/gromacs (source tree) Working dir: /opt/gromacs/build Command line: gmx --version GROMACS version: 2023-dev-20220118-fbf7230 GIT SHA1 hash: fbf723086ec6d21de5d1916397a326be8005541e 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to 1803419341 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 (5 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to -304614417 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 (4 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to 2146423675 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 (6 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to 2119120318 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 (11 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to -9568777 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 (11 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 2023-dev-20220118-fbf7230 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2023-dev-20220118-fbf7230 (single precision) Setting the LD random seed to -50724871 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 (4 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (45 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. (47 ms total) [ PASSED ] 21 tests. Summary: Gromacs commit fbf7230 works fine. Status: OK EndDate: 2022-01-24 11:10:17+00:00