Hi everyone,
I am trying to install gromacs 2021.3 GPU supported patched with plumed 2.7.2. However, when I tried ‘make check’ command, I got the following error
[ 0%] Built target gmx_objlib
[ 0%] Built target scanner
[ 0%] Generating release version information
– The source code for this GROMACS installation is different from the officially released version.
[ 0%] Built target release-version-info
[ 0%] Built target fftwBuild
[ 1%] Built target thread_mpi
[ 1%] Built target lmfit_objlib
[ 2%] Built target tng_io_obj
[ 2%] Built target tng_io_zlib
[ 16%] Built target linearalgebra
[ 16%] Built target modularsimulator
[ 16%] Linking CXX shared library …/…/lib/libgromacs_2021_plumed.so
[ 65%] Built target libgromacs
[ 65%] Built target view_objlib
[ 65%] Built target mdrun_objlib
[ 65%] Linking CXX executable …/…/bin/gmx_2021_plumed
[ 65%] Built target gmx
[ 65%] Built target gmxtests
[ 65%] Built target gtest
[ 65%] Built target gmock
[ 65%] Linking CXX shared library …/…/lib/libtestutils.so
[ 67%] Built target testutils
[ 67%] Built target mdrun_test_infrastructure
[ 67%] Linking CXX shared library …/…/lib/libgmxapi_2021_plumed.so
[ 68%] Built target gmxapi
[ 69%] Linking CXX executable …/…/…/…/…/bin/workflow-details-test
[ 69%] Built target workflow-details-test
[ 69%] Linking CXX shared library …/…/lib/libnblib.so
[ 70%] Built target nblib
[ 70%] Built target nblib_test_infrastructure
[ 70%] Linking CXX executable …/…/…/bin/nblib-integrator-test
[ 70%] Built target nblib-integrator-test
[ 70%] Linking CXX executable …/…/…/bin/methane-water-integration
[ 70%] Built target methane-water-integration
[ 70%] Linking CXX executable …/…/…/bin/argon-forces-integration
[ 70%] Built target argon-forces-integration
[ 72%] Linking CXX executable …/…/…/bin/nblib-setup-test
[ 72%] Built target nblib-setup-test
[ 72%] Linking CXX executable …/…/…/bin/nblib-integration-test
[ 73%] Built target nblib-integration-test
[ 73%] Built target nblib-tests
[ 73%] Linking CXX executable …/…/…/…/bin/nblib-listed-forces-test
[ 73%] Built target nblib-listed-forces-test
[ 73%] Linking CXX executable …/…/…/…/bin/nblib-util-test
[ 73%] Built target nblib-util-test
[ 73%] Linking CXX executable …/…/…/bin/testutils-mpi-test
[ 73%] Built target testutils-mpi-test
[ 73%] Linking CXX executable …/…/…/bin/testutils-test
[ 73%] Built target testutils-test
[ 73%] Linking CXX executable …/…/…/…/bin/utility-mpi-test
[ 73%] Built target utility-mpi-test
[ 73%] Linking CXX executable …/…/…/…/bin/utility-test
[ 74%] Built target utility-test
[ 74%] Linking CXX executable …/…/…/…/bin/mdlib-test
[ 75%] Built target mdlib-test
[ 77%] Linking CXX executable …/…/…/…/…/bin/awh-test
[ 77%] Built target awh-test
[ 78%] Linking CXX executable …/…/…/…/…/bin/density_fitting_applied_forces-test
[ 78%] Built target density_fitting_applied_forces-test
[ 78%] Linking CXX executable …/…/…/…/bin/applied_forces-test
[ 78%] Built target applied_forces-test
[ 78%] Linking CXX executable …/…/…/…/bin/listed_forces-test
[ 78%] Built target listed_forces-test
[ 78%] Built target onlinehelp-test-shared
[ 78%] Linking CXX executable …/…/…/…/bin/commandline-test
[ 78%] Built target commandline-test
[ 78%] Linking CXX executable …/…/…/…/bin/domdec-mpi-test
[ 78%] Built target domdec-mpi-test
[ 78%] Linking CXX executable …/…/…/…/bin/domdec-test
[ 78%] Built target domdec-test
[ 78%] Linking CXX executable …/…/…/…/bin/ewald-test
[ 79%] Built target ewald-test
[ 79%] Linking CXX executable …/…/…/…/bin/fft-test
[ 79%] Built target fft-test
[ 79%] Linking CXX executable …/…/…/…/bin/gpu_utils-test
[ 79%] Built target gpu_utils-test
[ 79%] Linking CXX executable …/…/…/…/bin/hardware-test
[ 79%] Built target hardware-test
[ 79%] Linking CXX executable …/…/…/…/bin/math-test
[ 81%] Built target math-test
[ 81%] Built target mdrunutility-test-shared
[ 81%] Linking CXX executable …/…/…/…/bin/mdrunutility-test
[ 81%] Built target mdrunutility-test
[ 81%] Linking CXX executable …/…/…/…/bin/mdrunutility-mpi-test
[ 82%] Built target mdrunutility-mpi-test
[ 82%] Linking CXX executable …/…/…/…/bin/mdspan-test
[ 82%] Built target mdspan-test
[ 82%] Linking CXX executable …/…/…/…/bin/mdtypes-test
[ 82%] Built target mdtypes-test
[ 82%] Linking CXX executable …/…/…/…/bin/onlinehelp-test
[ 83%] Built target onlinehelp-test
[ 83%] Linking CXX executable …/…/…/…/bin/options-test
[ 83%] Built target options-test
[ 83%] Linking CXX executable …/…/…/…/bin/pbcutil-test
[ 83%] Built target pbcutil-test
[ 84%] Linking CXX executable …/…/…/…/bin/random-test
[ 84%] Built target random-test
[ 84%] Linking CXX executable …/…/…/…/bin/restraintpotential-test
[ 84%] Built target restraintpotential-test
[ 84%] Linking CXX executable …/…/…/…/bin/table-test
[ 84%] Built target table-test
[ 84%] Linking CXX executable …/…/…/…/bin/taskassignment-test
[ 86%] Built target taskassignment-test
[ 86%] Linking CXX executable …/…/…/…/bin/topology-test
[ 87%] Built target topology-test
[ 87%] Linking CXX executable …/…/…/…/bin/pull-test
[ 87%] Built target pull-test
[ 87%] Linking CXX executable …/…/…/…/bin/simd-test
[ 88%] Built target simd-test
[ 88%] Linking CXX executable …/…/…/…/bin/compat-test
[ 88%] Built target compat-test
[ 88%] Linking CXX executable …/…/…/…/bin/gmxana-test
[ 88%] Built target gmxana-test
[ 88%] Linking CXX executable …/…/…/…/bin/pdb2gmx3-test
[ 88%] Built target pdb2gmx3-test
[ 88%] Linking CXX executable …/…/…/…/bin/pdb2gmx1-test
[ 89%] Built target pdb2gmx1-test
[ 91%] Linking CXX executable …/…/…/…/bin/gmxpreprocess-test
[ 91%] Built target gmxpreprocess-test
[ 91%] Linking CXX executable …/…/…/…/bin/pdb2gmx2-test
[ 91%] Built target pdb2gmx2-test
[ 91%] Linking CXX executable …/…/…/…/bin/correlations-test
[ 91%] Built target correlations-test
[ 91%] Built target analysisdata-test-shared
[ 91%] Linking CXX executable …/…/…/…/bin/analysisdata-test
[ 91%] Built target analysisdata-test
[ 91%] Linking CXX executable …/…/…/…/bin/coordinateio-test
[ 92%] Built target coordinateio-test
[ 92%] Linking CXX executable …/…/…/…/bin/trajectoryanalysis-test
[ 93%] Built target trajectoryanalysis-test
[ 93%] Linking CXX executable …/…/…/…/bin/energyanalysis-test
[ 93%] Built target energyanalysis-test
[ 93%] Linking CXX executable …/…/…/…/bin/tool-test
[ 93%] Built target tool-test
[ 93%] Linking CXX executable …/…/…/…/bin/fileio-test
[ 94%] Built target fileio-test
[ 94%] Linking CXX executable …/…/…/…/bin/selection-test
[ 94%] Built target selection-test
[ 94%] Linking CXX executable …/…/…/…/bin/mdrun-simulator-comparison-test
[ 94%] Built target mdrun-simulator-comparison-test
[ 94%] Linking CXX executable …/…/…/…/bin/mdrun-output-test
[ 94%] Built target mdrun-output-test
[ 94%] Linking CXX executable …/…/…/…/bin/mdrunfep-test
[ 94%] Built target mdrunfep-test
[ 94%] Linking CXX executable …/…/…/…/bin/mdrun-modules-test
[ 96%] Built target mdrun-modules-test
[ 96%] Linking CXX executable …/…/…/…/bin/mdrun-test
[ 97%] Built target mdrun-test
[ 97%] Linking CXX executable …/…/…/…/bin/mdrun-pme-test
[ 97%] Built target mdrun-pme-test
[ 97%] Linking CXX executable …/…/…/…/bin/mdrun-non-integrator-test
[ 98%] Built target mdrun-non-integrator-test
[ 98%] Linking CXX executable …/…/…/…/bin/mdrun-mpi-coordination-test
[ 98%] Built target mdrun-mpi-coordination-test
[ 98%] Linking CXX executable …/…/…/…/bin/mdrun-io-test
[ 98%] Built target mdrun-io-test
[ 98%] Linking CXX executable …/…/…/…/bin/mdrun-tpi-test
[ 98%] Built target mdrun-tpi-test
[ 98%] Linking CXX executable …/…/…/…/bin/mdrun-mpi-test
[ 98%] Built target mdrun-mpi-test
[ 98%] Linking CXX executable …/…/…/…/bin/mdrun-mpi-pme-test
[ 98%] Built target mdrun-mpi-pme-test
[ 98%] Linking CXX executable …/…/…/…/bin/gmxapi-test
[ 98%] Built target gmxapi-test
[100%] Linking CXX executable …/…/…/…/bin/gmxapi-mpi-test
[100%] Built target gmxapi-mpi-test
[100%] Linking CXX executable …/…/…/…/…/bin/workflow-details-mpi-test
[100%] Built target workflow-details-mpi-test
[100%] Built target tests
[100%] Running all tests except physical validation
Test project /scratch/panbazha/ngoquoc1/gromacs/gromacs-2021.3/build
Start 1: NbLibListedForcesTests
1/73 Test #1: NbLibListedForcesTests … Passed 5.48 sec
Start 2: NbLibSamplesTestArgon
2/73 Test #2: NbLibSamplesTestArgon … Passed 0.05 sec
Start 3: NbLibSamplesTestMethaneWater
3/73 Test #3: NbLibSamplesTestMethaneWater … Passed 0.05 sec
Start 4: NbLibUtilTests
4/73 Test #4: NbLibUtilTests … Passed 0.37 sec
Start 5: NbLibSetupTests
5/73 Test #5: NbLibSetupTests … Passed 0.36 sec
Start 6: NbLibIntegrationTests
6/73 Test #6: NbLibIntegrationTests … Passed 0.38 sec
Start 7: NbLibIntegratorTests
7/73 Test #7: NbLibIntegratorTests … Passed 0.37 sec
Start 8: TestUtilsUnitTests
8/73 Test #8: TestUtilsUnitTests … Passed 0.42 sec
Start 9: TestUtilsMpiUnitTests
make[3]: *** [CMakeFiles/run-ctest-nophys] Segmentation fault
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
make: *** [check] Error 2
Is anyone here know what is the problem? Afterwards, when I tried ‘make install’ command, the installation succeeded, and I can use the program seems to work well.
Thank you so much.