StartDate: 2024-04-17 06:52:41+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: 1a29073fbcb476dc3ab79655744d12eef97a2b59 CommitTime: 2024-04-16 12:53:47 +0200 CommitAuthor: marcella CommitSubject: E-field restart and output (#3354) #################### Building Image cp2k-gromacs #################### Dockerfile: /tools/docker/Dockerfile.test_gromacs Build-Path: / Build-Args: GIT_COMMIT_SHA=1a29073fbcb476dc3ab79655744d12eef97a2b59 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 394.2MB Step 1/41 : FROM ubuntu:22.04 22.04: Pulling from library/ubuntu 3c645031de29: Pulling fs layer 3c645031de29: Verifying Checksum 3c645031de29: Download complete 3c645031de29: Pull complete Digest: sha256:1b8d8ff4777f36f19bfe73ee4df61e3a0b789caeff29caa019539ec7c9a57f95 Status: Downloaded newer image for ubuntu:22.04 ---> 7af9ba4f0a47 Step 2/41 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> 9dd3c38d749f Step 3/41 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> 85614924da4a Step 4/41 : RUN ./install_requirements.sh ubuntu:22.04 ---> Using cache ---> 7aff2b7aa738 Step 5/41 : RUN mkdir scripts ---> Using cache ---> 396b1dbd6ede 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 ---> 647732b64fd5 Step 7/41 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> 55700dee0a5a Step 8/41 : RUN ./install_cp2k_toolchain.sh --install-all --with-gcc=system --dry-run ---> Using cache ---> 53d4008825ec Step 9/41 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> Using cache ---> b7ed63d2aec8 Step 10/41 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Using cache ---> ba960a28d000 Step 11/41 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> Using cache ---> 5e0dd371d8da Step 12/41 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Using cache ---> b6411bdd5988 Step 13/41 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> Using cache ---> a337dd578665 Step 14/41 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Using cache ---> a805edf5d445 Step 15/41 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> Using cache ---> 89c3fab60b10 Step 16/41 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Using cache ---> 11ede4addb4c Step 17/41 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> Using cache ---> 28d01e379245 Step 18/41 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Using cache ---> 432ae994d46f Step 19/41 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> Using cache ---> aa3695fb1a8a Step 20/41 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Using cache ---> 2385437ba30d Step 21/41 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> Using cache ---> 99c9de45acee Step 22/41 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Using cache ---> f51168b70480 Step 23/41 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> Using cache ---> 0d490d89a462 Step 24/41 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Using cache ---> bf61ef83c357 Step 25/41 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> Using cache ---> f54ba4d1feaf Step 26/41 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Using cache ---> 65095d18cd26 Step 27/41 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> Using cache ---> 3909634d023e Step 28/41 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Using cache ---> 3050171b81d5 Step 29/41 : WORKDIR /opt/cp2k ---> Using cache ---> b59dffc80ca7 Step 30/41 : COPY ./Makefile . ---> Using cache ---> 5dca7b701d23 Step 31/41 : COPY ./src ./src ---> Using cache ---> d0c9c8a14f50 Step 32/41 : COPY ./exts ./exts ---> Using cache ---> f47711eace6e Step 33/41 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> 97761cdad3ee Step 34/41 : RUN /bin/bash -c " mkdir -p arch && ln -vs /opt/cp2k-toolchain/install/arch/local.sdbg ./arch/" ---> Using cache ---> 3e223725512a Step 35/41 : COPY ./data ./data ---> Using cache ---> d88674c82e04 Step 36/41 : COPY ./tests ./tests ---> Using cache ---> 8e5c97c1ca54 Step 37/41 : COPY ./tools/regtesting ./tools/regtesting ---> Using cache ---> 184a745ff635 Step 38/41 : COPY ./tools/docker/scripts/test_gromacs.sh . ---> bad2b8259e0d Step 39/41 : RUN ./test_gromacs.sh 2>&1 | tee report.log ---> Running in 9b163bfd7c1b Compiling libcp2k... done. ========== Building Gromacs ========== Cloning Gromacs repository... done. Configuring Gromacs... done. Compiling Gromacs... done. 2024-04-17 07:02:20.687685: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-04-17 07:02:20.718956: 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 2024-04-17 07:02:20.719001: 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 2024-04-17 07:02:20.719023: 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-20240416-f6263bc (-: 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-20240416-f6263bc GIT SHA1 hash: f6263bc9625fa7a1203c6fbfdbb0374038654a1e 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 ========== 2024-04-17 07:02:21.096765: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-04-17 07:02:21.128393: 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 2024-04-17 07:02:21.128436: 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 2024-04-17 07:02:21.128459: 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to -1124349188 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to -1091602501 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 (61 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to 1073477621 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 (83 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to -538984473 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 (118 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to 734785407 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-20240416-f6263bc (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025-dev-20240416-f6263bc (single precision) Setting the LD random seed to -4661254 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 (78 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (351 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. (352 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 f6263bc works fine. Status: OK Removing intermediate container 9b163bfd7c1b ---> ad2a9422b705 Step 40/41 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 165e62cbcd54 Removing intermediate container 165e62cbcd54 ---> 1c3cd971225a Step 41/41 : ENTRYPOINT [] ---> Running in 85f680fc040a Removing intermediate container 85f680fc040a ---> 835f7ec0271a [Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed Successfully built 835f7ec0271a Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-gromacs:master Pushing new image... done. #################### Running Image cp2k-gromacs #################### EndDate: 2024-04-17 07:04:50+00:00