StartDate: 2024-11-04 06:13:57+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: af28e69c1374a8846f08d084605578e74af28564 CommitTime: 2024-11-03 21:10:32 +0100 CommitAuthor: Matthias Krack CommitSubject: Minor fixes and improvements #################### Building Image cp2k-gromacs #################### Dockerfile: /tools/docker/Dockerfile.test_gromacs Build-Path: / Build-Args: GIT_COMMIT_SHA=af28e69c1374a8846f08d084605578e74af28564 Build-Cache: Yes Populating docker build cache... done. DEPRECATED: The legacy builder is deprecated and will be removed in a future release. BuildKit is currently disabled; enable it by removing the DOCKER_BUILDKIT=0 environment-variable. Sending build context to Docker daemon 397.5MB Step 1/16 : FROM ubuntu:24.04 24.04: Pulling from library/ubuntu ff65ddf9395b: Pulling fs layer ff65ddf9395b: Verifying Checksum ff65ddf9395b: Download complete ff65ddf9395b: Pull complete Digest: sha256:99c35190e22d294cdace2783ac55effc69d32896daaa265f0bbedbcde4fbe3e5 Status: Downloaded newer image for ubuntu:24.04 ---> 59ab366372d5 Step 2/16 : RUN export DEBIAN_FRONTEND=noninteractive DEBCONF_NONINTERACTIVE_SEEN=true && apt-get update -qq && apt-get install -qq --no-install-recommends cmake less nano make ninja-build wget python3 ca-certificates gcc-13 g++-13 gfortran-13 libfftw3-dev libopenblas-dev libint2-dev libxc-dev libxsmm-dev libspglib-f08-dev && rm -rf /var/lib/apt/lists/* ---> Using cache ---> 62a2c962974b Step 3/16 : RUN ln -sf /usr/bin/gcc-13 /usr/local/bin/gcc && ln -sf /usr/bin/g++-13 /usr/local/bin/g++ && ln -sf /usr/bin/gfortran-13 /usr/local/bin/gfortran ---> Using cache ---> 579d4adb9a68 Step 4/16 : COPY ./tools/docker/scripts/install_dbcsr.sh ./ ---> Using cache ---> 13351d12026e Step 5/16 : RUN ./install_dbcsr.sh ---> Using cache ---> 96abd4453e45 Step 6/16 : WORKDIR /opt/cp2k ---> Using cache ---> 7e8f719d6c42 Step 7/16 : COPY ./src ./src ---> Using cache ---> 69d880be1b2b Step 8/16 : COPY ./data ./data ---> Using cache ---> cb76b90c9ceb Step 9/16 : COPY ./tests ./tests ---> Using cache ---> ddfa6834b335 Step 10/16 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> 263948eb3dbc Step 11/16 : COPY ./cmake ./cmake ---> Using cache ---> f354cddb10a5 Step 12/16 : COPY ./CMakeLists.txt . ---> Using cache ---> c32ad48e2d7b Step 13/16 : COPY ./tools/docker/scripts/build_cp2k_cmake.sh ./tools/docker/scripts/test_gromacs.sh ./ ---> Using cache ---> e676f2676bdb Step 14/16 : RUN ./test_gromacs.sh 2>&1 | tee report.log ---> Using cache ---> 77533437aad2 Step 15/16 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Using cache ---> 3ce9994ff7d3 Step 16/16 : ENTRYPOINT [] ---> Using cache ---> 915b9ce94d82 [Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed Successfully built 915b9ce94d82 Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-gromacs:master Pushing new image... done. #################### Running Image cp2k-gromacs #################### ==================== Building CP2K ==================== -- The Fortran compiler identification is GNU 13.2.0 -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/local/bin/gfortran - skipped -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Python: /usr/bin/python3 (found version "3.12.3") found components: Interpreter -- Checking for module 'openblas' -- Found openblas, version 0.3.26 -- Found OpenBLAS: /usr/include/x86_64-linux-gnu -- Found Blas: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so -- Found Lapack: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so -- Checking for module 'libxsmm' -- Found libxsmm, version 1.17.0 -- Checking for module 'libxsmmext' -- Found libxsmmext, version 1.17.0 -- Checking for module 'libxsmmf' -- Found libxsmmf, version 1.17.0 -- Checking for module 'libxsmmnoblas' -- Found libxsmmnoblas, version 1.17.0 -- Found LibXSMM: /usr/include -- Using libxsmm for Small Matrix Multiplication -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: Fortran C CXX -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Checking for modules 'libxcf03;libxc>=6' -- Package dependency requirement 'libxc >= 6' could not be satisfied. Package 'libxc' has version '5.2.3', required version is '>= 6' -- Found LibXC: ON (Required is exact version "6") -- Checking for one of the modules 'fftw3' -- Checking for one of the modules 'fftw3f' -- Checking for one of the modules 'fftw3l' -- Checking for one of the modules 'fftw3q' -- Found Fftw: /usr/include -- Checking for module 'libint2' -- Found libint2, version 2.7.2 -- Found Libint2: /usr/include;/usr/include/libint2;/usr/include/eigen3 -- Setting build type to 'Release' as none was specified. -- Performing Test f2008-norm2 -- Performing Test f2008-norm2 - Success -- Performing Test f2008-block_construct -- Performing Test f2008-block_construct - Success -- Performing Test f2008-contiguous -- Performing Test f2008-contiguous - Success -- Performing Test f95-reshape-order-allocatable -- Performing Test f95-reshape-order-allocatable - Success -- FYPP preprocessor found. -------------------------------------------------------------------- - - - Summary of enabled dependencies - - - -------------------------------------------------------------------- - BLAS AND LAPACK - vendor : OpenBLAS - include directories : - libraries : /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so - LIBXC (note to package managers : libxc can be build with cmake as well) - include directories : /usr/include - libraries : /usr/lib/x86_64-linux-gnu/libxcf03.so;/usr/lib/x86_64-linux-gnu/libxc.so - FFTW3 - include directories : /usr/include - libraries : /usr/lib/x86_64-linux-gnu/libfftw3.so - libxsmm - include directories : /usr/include - libraries : /usr/lib/libxsmmext.a;/usr/lib/libxsmm.a;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libc.so;/usr/lib/libxsmmf.a;/usr/lib/libxsmm.a;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libc.so - libint2 - include directories : /usr/include;/usr/include/libint2;/usr/include/eigen3 - libraries : /usr/lib/x86_64-linux-gnu/libint2.so -------------------------------------------------------------------- - - - List of dependencies not included in this build - - - -------------------------------------------------------------------- - MPI - DFTD4 - SIRIUS - SPGLIB - COSMA - SPLA - GPU acceleration is disabled - ELPA - DLAF - PLUMED - QUIP - LIBVORI - PEXSI - SUPERLU - libtorch To run the regtests you need to run the following commands cd .. export CP2K_DATA_DIR=/opt/cp2k/data/ ./tests/do_regtest.py /opt/cp2k/build/bin ssmp -- Configuring done (2.7s) -- Generating done (0.2s) -- Build files have been written to: /opt/cp2k/build Compiling cp2k...done. ========== Installing Dependencies ========== debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package perl-modules-5.38. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31248 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2build2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2build2) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.23-5.1build1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1build1) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.23-5.1build1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../3-libperl5.38t64_5.38.2-3.2build2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2build2) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.38.2-3.2build2_amd64.deb ... Unpacking perl (5.38.2-3.2build2) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../5-libcurl3t64-gnutls_8.5.0-2ubuntu10.4_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10.4) ... Selecting previously unselected package liberror-perl. Preparing to unpack .../6-liberror-perl_0.17029-2_all.deb ... Unpacking liberror-perl (0.17029-2) ... Selecting previously unselected package git-man. Preparing to unpack .../7-git-man_1%3a2.43.0-1ubuntu7.1_all.deb ... Unpacking git-man (1:2.43.0-1ubuntu7.1) ... Selecting previously unselected package git. Preparing to unpack .../8-git_1%3a2.43.0-1ubuntu7.1_amd64.deb ... Unpacking git (1:2.43.0-1ubuntu7.1) ... Setting up libgdbm6t64:amd64 (1.23-5.1build1) ... Setting up libgdbm-compat4t64:amd64 (1.23-5.1build1) ... Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10.4) ... Setting up perl-modules-5.38 (5.38.2-3.2build2) ... Setting up git-man (1:2.43.0-1ubuntu7.1) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2build2) ... Setting up perl (5.38.2-3.2build2) ... Setting up liberror-perl (0.17029-2) ... Setting up git (1:2.43.0-1ubuntu7.1) ... Processing triggers for libc-bin (2.39-0ubuntu8.3) ... ========== Building Gromacs ========== Cloning Gromacs repository... done. Configuring Gromacs... done. Compiling Gromacs... done. :-) GROMACS - gmx, 2025.0-dev-20241030-e63e287 (-: Executable: /opt/gromacs/build/./bin/gmx Data prefix: /opt/gromacs (source tree) Working dir: /opt/gromacs/build Command line: gmx --version GROMACS version: 2025.0-dev-20241030-e63e287 GIT SHA1 hash: e63e287183b856b403c217f815777d056838241d Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: disabled SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.10-sse2-avx-avx2-avx2_128 GPU FFT library: none Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: C compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wpedantic -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: C++ compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wpedantic -Wundef -Wstringop-truncation -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG BLAS library: External - detected on the system LAPACK library: External - detected on the system ========== 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to 1777516530 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' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (4 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to 2147056957 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' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to -268534381 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' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to -142608391 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' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/alanine_vacuo.gro' 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 1.021 nm, buffer size 0.021 nm Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 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 (8 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to -219087361 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... Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/alanine_vacuo.gro' 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 1.023 nm, buffer size 0.023 nm Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 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 (7 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 The integrator does not provide a ensemble temperature, there is no system ensemble temperature 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 2025.0-dev-20241030-e63e287 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-dev-20241030-e63e287 (single precision) Setting the LD random seed to -532625 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 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 (2 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (29 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. (32 ms total) [ PASSED ] 21 tests. Summary: Gromacs commit e63e287 works fine. (cached) Status: OK EndDate: 2024-11-04 06:16:10+00:00