StartDate: 2024-02-28 06:45:16+00:00
CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled)

CommitSHA: 904d571b43f5f0873637c980131f2c93e7676bc7
CommitTime: 2024-02-27 11:37:46 +0100
CommitAuthor: Juerg Hutter
CommitSubject: Primitives for MinBas expansion can be set in input (#3288)


#################### Building Image cp2k-gromacs ####################
Dockerfile: /tools/docker/Dockerfile.test_gromacs
Build-Path: /
Build-Args: GIT_COMMIT_SHA=904d571b43f5f0873637c980131f2c93e7676bc7
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  393.7MB

Step 1/41 : FROM ubuntu:22.04
22.04: Pulling from library/ubuntu
01007420e9b0: Pulling fs layer
01007420e9b0: Verifying Checksum
01007420e9b0: Download complete
01007420e9b0: Pull complete
Digest: sha256:f9d633ff6640178c2d0525017174a688e2c1aef28f0a0130b26bd5554491f0da
Status: Downloaded newer image for ubuntu:22.04
 ---> 3db8720ecbf5
Step 2/41 : WORKDIR /opt/cp2k-toolchain
 ---> Using cache
 ---> c91877cf7c4f
Step 3/41 : COPY ./tools/toolchain/install_requirements*.sh ./
 ---> Using cache
 ---> 40cd32e951b0
Step 4/41 : RUN ./install_requirements.sh ubuntu:22.04
 ---> Using cache
 ---> 0e0c260a973e
Step 5/41 : RUN mkdir scripts
 ---> Using cache
 ---> c18ee2447245
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
 ---> 50a53065b028
Step 7/41 : COPY ./tools/toolchain/install_cp2k_toolchain.sh .
 ---> Using cache
 ---> 410cc668ef16
Step 8/41 : RUN ./install_cp2k_toolchain.sh     --install-all     --with-gcc=system     --dry-run
 ---> Using cache
 ---> ef458af826b9
Step 9/41 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/
 ---> Using cache
 ---> 5b5e2bc49cd5
Step 10/41 : RUN  ./scripts/stage0/install_stage0.sh && rm -rf ./build
 ---> Using cache
 ---> b6701df80a4f
Step 11/41 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/
 ---> Using cache
 ---> 65bb47d5e0be
Step 12/41 : RUN  ./scripts/stage1/install_stage1.sh && rm -rf ./build
 ---> Using cache
 ---> 3235032c243b
Step 13/41 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/
 ---> Using cache
 ---> 9fdaac814822
Step 14/41 : RUN  ./scripts/stage2/install_stage2.sh && rm -rf ./build
 ---> Using cache
 ---> 89a5d839f744
Step 15/41 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/
 ---> Using cache
 ---> d4181b8c9115
Step 16/41 : RUN  ./scripts/stage3/install_stage3.sh && rm -rf ./build
 ---> Using cache
 ---> a200824ab62c
Step 17/41 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/
 ---> Using cache
 ---> cf4e3530cfac
Step 18/41 : RUN  ./scripts/stage4/install_stage4.sh && rm -rf ./build
 ---> Using cache
 ---> b7543240dd55
Step 19/41 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/
 ---> Using cache
 ---> 7661f7b25b97
Step 20/41 : RUN  ./scripts/stage5/install_stage5.sh && rm -rf ./build
 ---> Using cache
 ---> 2b02d0f56252
Step 21/41 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/
 ---> Using cache
 ---> c6fa05294c14
Step 22/41 : RUN  ./scripts/stage6/install_stage6.sh && rm -rf ./build
 ---> Using cache
 ---> 57c0d372fca0
Step 23/41 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/
 ---> Using cache
 ---> c6bed1fbbe7e
Step 24/41 : RUN  ./scripts/stage7/install_stage7.sh && rm -rf ./build
 ---> Using cache
 ---> 3c67707a23a0
Step 25/41 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/
 ---> Using cache
 ---> b8ef848c5e78
Step 26/41 : RUN  ./scripts/stage8/install_stage8.sh && rm -rf ./build
 ---> Using cache
 ---> 61b028d7894a
Step 27/41 : COPY ./tools/toolchain/scripts/arch_base.tmpl      ./tools/toolchain/scripts/generate_arch_files.sh      ./scripts/
 ---> Using cache
 ---> 7eda2a584141
Step 28/41 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build
 ---> Using cache
 ---> 7ac6d70c4f6f
Step 29/41 : WORKDIR /opt/cp2k
 ---> Using cache
 ---> 1c08b4b239c6
Step 30/41 : COPY ./Makefile .
 ---> Using cache
 ---> f0c5e49b29f4
Step 31/41 : COPY ./src ./src
 ---> Using cache
 ---> 20f6ab5945bc
Step 32/41 : COPY ./exts ./exts
 ---> Using cache
 ---> b6fb8553e726
Step 33/41 : COPY ./tools/build_utils ./tools/build_utils
 ---> Using cache
 ---> 264dd36a6fce
Step 34/41 : RUN /bin/bash -c "     mkdir -p arch &&     ln -vs /opt/cp2k-toolchain/install/arch/local.sdbg ./arch/"
 ---> Using cache
 ---> 591e4dc7f572
Step 35/41 : COPY ./data ./data
 ---> Using cache
 ---> d68875b5edc4
Step 36/41 : COPY ./tests ./tests
 ---> Using cache
 ---> 851fe0561e8a
Step 37/41 : COPY ./tools/regtesting ./tools/regtesting
 ---> Using cache
 ---> abf336daad0c
Step 38/41 : COPY ./tools/docker/scripts/test_gromacs.sh .
 ---> c92522c6017a
Step 39/41 : RUN ./test_gromacs.sh 2>&1 | tee report.log
 ---> Running in 0097b34a8fc7
Compiling libcp2k... done.

========== Building Gromacs ==========
Cloning Gromacs repository... done.
Configuring Gromacs... done.
Compiling Gromacs... done.


2024-02-28 06:54:08.242192: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-02-28 06:54:08.274712: 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
2024-02-28 06:54:08.274739: 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
2024-02-28 06:54:08.274762: 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-20240227-711ed1c (-:

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-20240227-711ed1c
GIT SHA1 hash:       711ed1cb2b0364df62c3d15d0117316f9215a10d
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 ==========
2024-02-28 06:54:08.643238: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-02-28 06:54:08.674872: 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
2024-02-28 06:54:08.674899: 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
2024-02-28 06:54:08.674922: 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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -411186065

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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -965158929

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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -1110442006

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 (1 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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -747216129

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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -1592323

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-20240227-711ed1c (single precision)
Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025-dev-20240227-711ed1c (single precision)
Setting the LD random seed to -75501770

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 (20 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. (21 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 711ed1c works fine.
Status: OK

Removing intermediate container 0097b34a8fc7
 ---> 4f4bd2f8ee65
Step 40/41 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/'
 ---> Running in 14af607eaa96
Removing intermediate container 14af607eaa96
 ---> 88c4e04209ea
Step 41/41 : ENTRYPOINT []
 ---> Running in d8f1f4260e39
Removing intermediate container d8f1f4260e39
 ---> 1b6c8d8a4c3c
[Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed
Successfully built 1b6c8d8a4c3c
Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-gromacs:master

Pushing new image... done.

#################### Running Image cp2k-gromacs ####################

EndDate: 2024-02-28 06:56:33+00:00