Gromacs All Test Fails

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1

GROMACS version: 2024.1
GROMACS modification: No
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Hi everyone,

I am trying to install gromacs-2024.1 on a new system with Rocky-Linux OS on RTX 4070 Ti GPU. I have installed the Cuda-12.4 toolkit.
I have gcc compilers installed - gcc-8.5 and gcc-12, I am supplying the gcc-12 for installation.

I am running the following commands in that order:

1. cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=~/.local/gromacs 
 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
2. make -j$(nproc)
3. make check

After the 3rd step, it says all the tests have failed with the following output:

0% tests passed, 88 tests failed out of 88

Label Time Summary:
GTest              =   0.13 sec*proc (83 tests)
IntegrationTest    =   0.04 sec*proc (26 tests)
MpiTest            =   0.03 sec*proc (19 tests)
QuickGpuTest       =   0.03 sec*proc (18 tests)
SlowGpuTest        =   0.27 sec*proc (17 tests)
SlowTest           =   0.02 sec*proc (13 tests)
UnitTest           =   0.07 sec*proc (44 tests)

Total Test time (real) =   0.40 sec

The following tests FAILED:
	  1 - GmxapiExternalInterfaceTests (Failed)
	  2 - GmxapiInternalInterfaceTests (Failed)
	  3 - NbLibListedForcesTests (Failed)
	  4 - NbLibSamplesTestArgon (Failed)
	  5 - NbLibSamplesTestMethaneWater (Failed)
	  6 - NbLibUtilTests (Failed)
	  7 - NbLibSetupTests (Failed)
	  8 - NbLibTprTests (Failed)
	  9 - NbLibIntegrationTests (Failed)
	 10 - NbLibIntegratorTests (Failed)
	 11 - TestUtilsUnitTests (Failed)
	 12 - TestUtilsMpiUnitTests (Failed)
	 13 - UtilityUnitTests (Failed)
	 14 - UtilityMpiUnitTests (Failed)
	 15 - GmxlibTests (Failed)
	 16 - MdlibUnitTest (Failed)
	 17 - AwhTest (Failed)
	 18 - DensityFittingAppliedForcesUnitTest (Failed)
	 19 - QMMMAppliedForcesUnitTest (Failed)
	 20 - ColvarsAppliedForcesUnitTest (Failed)
	 21 - AppliedForcesUnitTest (Failed)
	 22 - ListedForcesTest (Failed)
	 23 - NbnxmTests (Failed)
	 24 - CommandLineUnitTests (Failed)
	 25 - DomDecTests (Failed)
	 26 - DomDecMpiTests (Failed)
	 27 - EwaldUnitTests (Failed)
	 28 - FFTUnitTests (Failed)
	 29 - GpuUtilsUnitTests (Failed)
	 30 - HardwareUnitTests (Failed)
	 31 - MathUnitTests (Failed)
	 32 - MdrunUtilityUnitTests (Failed)
	 33 - MdrunUtilityMpiUnitTests (Failed)
	 34 - MDSpanTests (Failed)
	 35 - MdtypesUnitTest (Failed)
	 36 - OnlineHelpUnitTests (Failed)
	 37 - OptionsUnitTests (Failed)
	 38 - PbcutilUnitTest (Failed)
	 39 - RandomUnitTests (Failed)
	 40 - RestraintTests (Failed)
	 41 - TableUnitTests (Failed)
	 42 - TaskAssignmentUnitTests (Failed)
	 43 - GmxTimingTests (Failed)
	 44 - TopologyTest (Failed)
	 45 - PullTest (Failed)
	 46 - SimdUnitTests (Failed)
	 47 - CompatibilityHelpersTests (Failed)
	 48 - GmxAnaTest (Failed)
	 49 - GmxPreprocessTests (Failed)
	 50 - Pdb2gmx1Test (Failed)
	 51 - Pdb2gmx2Test (Failed)
	 52 - Pdb2gmx3Test (Failed)
	 53 - CorrelationsTest (Failed)
	 54 - AnalysisDataUnitTests (Failed)
	 55 - CoordinateIOTests (Failed)
	 56 - TrajectoryAnalysisUnitTests (Failed)
	 57 - EnergyAnalysisUnitTests (Failed)
	 58 - ToolUnitTests (Failed)
	 59 - FileIOTests (Failed)
	 60 - SelectionUnitTests (Failed)
	 61 - MdrunOutputTests (Failed)
	 62 - MdrunModulesTests (Failed)
	 63 - MdrunIOTests (Failed)
	 64 - MdrunTestsOneRank (Failed)
	 65 - MdrunTestsTwoRanks (Failed)
	 66 - MdrunSingleRankAlgorithmsTests (Failed)
	 67 - MdrunNonIntegratorTests (Failed)
	 68 - MdrunTpiTests (Failed)
	 69 - MdrunMpiTests (Failed)
	 70 - MdrunMultiSimTests (Failed)
	 71 - MdrunMultiSimReplexTests (Failed)
	 72 - MdrunMultiSimReplexEquivalenceTests (Failed)
	 73 - MdrunMpi1RankPmeTests (Failed)
	 74 - MdrunMpi2RankPmeTests (Failed)
	 75 - MdrunCoordinationBasicTests1Rank (Failed)
	 76 - MdrunCoordinationBasicTests2Ranks (Failed)
	 77 - MdrunCoordinationCouplingTests1Rank (Failed)
	 78 - MdrunCoordinationCouplingTests2Ranks (Failed)
	 79 - MdrunCoordinationConstraintsTests1Rank (Failed)
	 80 - MdrunCoordinationConstraintsTests2Ranks (Failed)
	 81 - MdrunFEPTests (Failed)
	 82 - MdrunPullTests (Failed)
	 83 - MdrunRotationTests (Failed)
	 84 - MdrunSimulatorComparison (Failed)
	 85 - MdrunVirtualSiteTests (Failed)
	 86 - regressiontests/complex (Failed)
	 87 - regressiontests/freeenergy (Failed)
	 88 - regressiontests/essentialdynamics (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:71: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:3287: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:3320: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:628: check] Error 2

Can someone please help me with figuring out what is wrong in the installation and how to correct it?

Thanks, and regards,
Chaitanya

2

Hi Chaitanya,
It’s a bit hard to tell what’s wrong from this information. Can you provide some more information from the error logs?

3

Hi Cathrine,

I am not sure where the error log files are present. Can you guide me?

-Thanks,
Chaitanya

4

I haven’t worked with Rocky Linux but I remember getting alot of errors on Ubuntu which resulted in tests failing at a later stage. What worked for me was simple: I installed with higher level privileges (using sudo, e.g. sudo cmake …, sudo make, sudo make install).

Another thing to look out is the errors/messages/warnings during cmake and make steps.

5

Hi @rpsingh ,

I will try to use sudo for installation.

Thanks for the suggestion.

-Chaitanya

6

Hi @rpsingh, @cathrine

Thanks for replying to my query.

Regarding Cathrine’s reply: I found these few lines at the beginning of the make check output which might contain some clues -

-- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.11", minimum required is "3.7")
-- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway.  If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on.
-- Checking for module 'mpi-cxx'
--   Package 'mpi-cxx', required by 'virtual:world', not found
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) 
-- Could NOT find MPI (missing: MPI_CXX_FOUND CXX) 
-- Did not detect build CPU features - detection program did not run successfully
-- Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35
-- Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35 - No
-- Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37
-- Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37 - No
-- Did not detect build CPU vendor - detection program did not run successfully
-- Did not detect build CPU brand - detection program did not run successfully
-- Did not detect build CPU family - detection program did not run successfully
-- Did not detect build CPU model - detection program did not run successfully
-- Did not detect build CPU stepping - detection program did not run successfully
-- Did not detect build CPU features - detection program did not run successfully
-- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: 
-- Configuring done (0.9s)
-- Generating done (0.4s)

I also tried to build using sudo privileges, but it still fails all the tests.

Please let me know if you have anymore suggestions on how to resolve this issue?

Thanks and regards,
Chaitanya

7

Dear Chaitanya,
Have you tried to do a standard quick-and-dirty installation as described in the GROMACS manual: Installation guide - GROMACS 2024.4 documentation ?
We can remove this installation later, but it would be good to see if any of your extra cmake flags might be causing problems.

8

Dear @cathrine

Thank you for your reply.
Apologies for replying so late.

But I abandoned rocky linux for ubuntu system as I was facing issues with almost all the software installations. The installation for ubuntu went smoothly as expected.

Thanks, and regards,
Chaitanya