StartDate: 2024-03-15 07:14:43+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: ae6dcbd3afce63fdb1f8314afc9b8411b443fd65 CommitTime: 2024-03-14 11:15:03 +0100 CommitAuthor: Juerg Hutter CommitSubject: TDDFT State Following (#3320) #################### Building Image cp2k-gromacs #################### Dockerfile: /tools/docker/Dockerfile.test_gromacs Build-Path: / Build-Args: GIT_COMMIT_SHA=ae6dcbd3afce63fdb1f8314afc9b8411b443fd65 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 394.1MB Step 1/41 : FROM ubuntu:22.04 22.04: Pulling from library/ubuntu bccd10f490ab: Pulling fs layer bccd10f490ab: Verifying Checksum bccd10f490ab: Download complete bccd10f490ab: Pull complete Digest: sha256:77906da86b60585ce12215807090eb327e7386c8fafb5402369e421f44eff17e Status: Downloaded newer image for ubuntu:22.04 ---> ca2b0f26964c Step 2/41 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> 03d16d9e2c6a Step 3/41 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> 72223eb0b8d0 Step 4/41 : RUN ./install_requirements.sh ubuntu:22.04 ---> Using cache ---> 432bb79a897a Step 5/41 : RUN mkdir scripts ---> Using cache ---> 1bac2e842a38 Step 6/41 : COPY ./tools/toolchain/scripts/VERSION ./tools/toolchain/scripts/parse_if.py ./tools/toolchain/scripts/tool_kit.sh ./tools/toolchain/scripts/common_vars.sh ./tools/toolchain/scripts/signal_trap.sh ./tools/toolchain/scripts/get_openblas_arch.sh ./scripts/ ---> Using cache ---> 94fa08efe2f0 Step 7/41 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> a9437683062a Step 8/41 : RUN ./install_cp2k_toolchain.sh --install-all --with-gcc=system --dry-run ---> Using cache ---> 12ff9cf83aed Step 9/41 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> Using cache ---> 6e9f97374a01 Step 10/41 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Using cache ---> a08edad7e3e5 Step 11/41 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> Using cache ---> 63778cccdf7f Step 12/41 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Using cache ---> e538b9780c22 Step 13/41 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> Using cache ---> 0e32b0cd01a2 Step 14/41 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Using cache ---> a06fd154f6ad Step 15/41 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> Using cache ---> 7db7df61870f Step 16/41 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Using cache ---> 77a4daa79489 Step 17/41 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> Using cache ---> 4a309c10153c Step 18/41 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Using cache ---> 75034c85a6d6 Step 19/41 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> Using cache ---> c60a8852e081 Step 20/41 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Using cache ---> 0b1a3154e422 Step 21/41 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> Using cache ---> ebc0b9070a55 Step 22/41 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Using cache ---> f9e582c35689 Step 23/41 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> Using cache ---> 513b1c38b831 Step 24/41 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Using cache ---> 3fb00d8c4d90 Step 25/41 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> Using cache ---> f81cc7aac257 Step 26/41 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Using cache ---> 0288ff6de7ea Step 27/41 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> Using cache ---> 02efd2668a6b Step 28/41 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Using cache ---> 6b70677d3992 Step 29/41 : WORKDIR /opt/cp2k ---> Using cache ---> 1d85531d5bbe Step 30/41 : COPY ./Makefile . ---> Using cache ---> 6c62f8f7257f Step 31/41 : COPY ./src ./src ---> Using cache ---> 240a5a84a66e Step 32/41 : COPY ./exts ./exts ---> Using cache ---> 262d412e13fb Step 33/41 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> 48b43f5d84bc Step 34/41 : RUN /bin/bash -c " mkdir -p arch && ln -vs /opt/cp2k-toolchain/install/arch/local.sdbg ./arch/" ---> Using cache ---> 36897fd22974 Step 35/41 : COPY ./data ./data ---> Using cache ---> b00962f6085f Step 36/41 : COPY ./tests ./tests ---> Using cache ---> d3d8d9377c92 Step 37/41 : COPY ./tools/regtesting ./tools/regtesting ---> Using cache ---> 8df9e78f5ee8 Step 38/41 : COPY ./tools/docker/scripts/test_gromacs.sh . ---> 53d5b6863abb Step 39/41 : RUN ./test_gromacs.sh 2>&1 | tee report.log ---> Running in edab3784d32a Compiling libcp2k... done. ========== Building Gromacs ========== Cloning Gromacs repository... done. Configuring Gromacs... done. Compiling Gromacs... done. 2024-03-15 07:23:56.184575: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-15 07:23:56.222594: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered 2024-03-15 07:23:56.222647: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered 2024-03-15 07:23:56.222672: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered DeePMD-kit: Cannot find libcudart.so.11.0 implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFatBinary', library failed to load implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFunction', library failed to load implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFatBinaryEnd', library failed to load implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaUnregisterFatBinary', library failed to load :-) GROMACS - gmx, 2025-dev-20240314-d8d6543 (-: Executable: /opt/gromacs/build/./bin/gmx Data prefix: /opt/gromacs (source tree) Working dir: /opt/gromacs/build Command line: gmx --version GROMACS version: 2025-dev-20240314-d8d6543 GIT SHA1 hash: d8d6543db04563cb15f71c90ffb5ed2fda092bce 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-3.3.8-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: /usr/bin/gcc GNU 11.4.0 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 -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -O3 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 11.4.0 C++ compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -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 ========== 2024-03-15 07:23:56.704609: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-15 07:23:56.737715: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered 2024-03-15 07:23:56.737763: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered 2024-03-15 07:23:56.737782: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered DeePMD-kit: Cannot find libcudart.so.11.0 implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFatBinary', library failed to load implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFunction', library failed to load implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaRegisterFatBinaryEnd', library failed to load [==========] 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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to -1161896417 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 (2 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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to -1158152386 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 (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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to -1090913689 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 (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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to -412590211 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 1.021 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 (5 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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to 1527536318 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 1.023 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 (6 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-dev-20240314-d8d6543 (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025-dev-20240314-d8d6543 (single precision) Setting the LD random seed to -1322394953 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 (2 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (21 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 (0 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. (22 ms total) [ PASSED ] 21 tests. implib-gen: libcudart.so.11.0: failed to load library 'libcudart.so.11.0' via callback 'DP_cudart_dlopen' implib-gen: libcudart.so.11.0: failed to resolve symbol '__cudaUnregisterFatBinary', library failed to load Summary: Gromacs commit d8d6543 works fine. Status: OK Removing intermediate container edab3784d32a ---> daf31f33b47a Step 40/41 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 14838ee9dcda Removing intermediate container 14838ee9dcda ---> 7d8c4a887419 Step 41/41 : ENTRYPOINT [] ---> Running in 45148735afbf Removing intermediate container 45148735afbf ---> 6539b76d326c [Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed Successfully built 6539b76d326c Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-gromacs:master Pushing new image... done. #################### Running Image cp2k-gromacs #################### EndDate: 2024-03-15 07:26:23+00:00