Installation Issues with 'make check'

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No
On a Rocky Linux machine.

Hello everyone. These are the instructions that are given to install Gromacs:
tar xfz gromacs-2023.1.tar.gz
cd gromacs-2023.1
mkdir build
cd build
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

I have made it all the way to the ‘make check’ without errors. But when ‘make check’ is done running, it says that 87 out of 87 tests have failed. Any ideas on how to proceed? Here is a snippet of what my output looks like:

0% tests passed, 87 tests failed out of 87

Label Time Summary:
GTest = 0.03 secproc (81 tests)
IntegrationTest = 0.01 secproc (25 tests)
MpiTest = 0.01 secproc (19 tests)
QuickGpuTest = 0.01 secproc (17 tests)
SlowGpuTest = 0.11 secproc (18 tests)
SlowTest = 0.01 secproc (13 tests)
UnitTest = 0.02 sec*proc (43 tests)

Total Test time (real) = 0.15 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 - AppliedForcesUnitTest (Failed)
21 - ListedForcesTest (Failed)
22 - NbnxmTests (Failed)
23 - CommandLineUnitTests (Failed)
24 - DomDecTests (Failed)
25 - DomDecMpiTests (Failed)
26 - EwaldUnitTests (Failed)
27 - FFTUnitTests (Failed)
28 - GpuUtilsUnitTests (Failed)
29 - HardwareUnitTests (Failed)
30 - MathUnitTests (Failed)
31 - MdrunUtilityUnitTests (Failed)
32 - MdrunUtilityMpiUnitTests (Failed)
33 - MDSpanTests (Failed)
34 - MdtypesUnitTest (Failed)
35 - OnlineHelpUnitTests (Failed)
36 - OptionsUnitTests (Failed)
37 - PbcutilUnitTest (Failed)
38 - RandomUnitTests (Failed)
39 - RestraintTests (Failed)
40 - TableUnitTests (Failed)
41 - TaskAssignmentUnitTests (Failed)
42 - GmxTimingTests (Failed)
43 - TopologyTest (Failed)
44 - PullTest (Failed)
45 - SimdUnitTests (Failed)
46 - CompatibilityHelpersTests (Failed)
47 - GmxAnaTest (Failed)
48 - GmxPreprocessTests (Failed)
49 - Pdb2gmx1Test (Failed)
50 - Pdb2gmx2Test (Failed)
51 - Pdb2gmx3Test (Failed)
52 - CorrelationsTest (Failed)
53 - AnalysisDataUnitTests (Failed)
54 - CoordinateIOTests (Failed)
55 - TrajectoryAnalysisUnitTests (Failed)
56 - EnergyAnalysisUnitTests (Failed)
57 - ToolUnitTests (Failed)
58 - FileIOTests (Failed)
59 - SelectionUnitTests (Failed)
60 - MdrunOutputTests (Failed)
61 - MdrunModulesTests (Failed)
62 - MdrunIOTests (Failed)
63 - MdrunTestsOneRank (Failed)
64 - MdrunTestsTwoRanks (Failed)
65 - MdrunSingleRankAlgorithmsTests (Failed)
66 - MdrunNonIntegratorTests (Failed)
67 - MdrunTpiTests (Failed)
68 - MdrunMpiTests (Failed)
69 - MdrunMultiSimTests (Failed)
70 - MdrunMultiSimReplexTests (Failed)
71 - MdrunMultiSimReplexEquivalenceTests (Failed)
72 - MdrunMpi1RankPmeTests (Failed)
73 - MdrunMpi2RankPmeTests (Failed)
74 - MdrunCoordinationBasicTests1Rank (Failed)
75 - MdrunCoordinationBasicTests2Ranks (Failed)
76 - MdrunCoordinationCouplingTests1Rank (Failed)
77 - MdrunCoordinationCouplingTests2Ranks (Failed)
78 - MdrunCoordinationConstraintsTests1Rank (Failed)
79 - MdrunCoordinationConstraintsTests2Ranks (Failed)
80 - MdrunFEPTests (Failed)
81 - MdrunPullTests (Failed)
82 - MdrunSimulatorComparison (Failed)
83 - MdrunVirtualSiteTests (Failed)
84 - regressiontests/complex (Failed)
85 - regressiontests/freeenergy (Failed)
86 - regressiontests/rotation (Failed)
87 - 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/Makefile2:3484: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2706: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:342: check] Error 2

2

Hi!

There should have been some kind of error output before what you posted. Please share the full log.

You can also run any individual test (e.g., ./bin/random-test), and check the output.

3

We get errors that look like this but for all 87 tests.

Start 1: GmxapiExternalInterfaceTests
1/87 Test #1: GmxapiExternalInterfaceTests …***Failed 0.01 sec
/home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by /home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test) /home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26’ not found (required by /home/exx/Downloads/gromacs-2023.1/build/lib/libgmxapi.so.0)
/home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by /home/exx/Downloads/gromacs-2023.1/build/lib/libgromacs.so.8) /home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26’ not found (required by /home/exx/Downloads/gromacs-2023.1/build/lib/libgtest.so.1.11.0)
/home/exx/Downloads/gromacs-2023.1/build/bin/gmxapi-test: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26’ not found (required by /home/exx/Downloads/gromacs-2023.1/build/lib/libmuparser.so.2)

Abnormal return value for ‘gmx grompp -f /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/essentialdynamics/linfix/grompp.mdp -c /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/essentialdynamics/linfix/conf -r /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/essentialdynamics/linfix/conf -p /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err’ was 1
Use of uninitialized value in addition (+) at /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/gmxtest.pl line 1916.
FAILED: Can not read sam.edi at /home/exx/Downloads/gromacs-2023.1/build/tests/regressiontests-2023.1/gmxtest.pl line 1427.

4

Looks like you have a partially broken compiler/stdlibrary combination on your system.

I don’t have Rocky Linux readily available for testing, but Googling “version GLIBCXX_3.4.26’ not found” produces quite a lot of results, including the ones for Rocky Linux. I suggest trying to install the missing packages.

After that, it might be helpful to completely remove GROMACS’s build directory and start from scratch, to avoid any leftover cached configuration values.

5

hi everyone, Even i face the following issues while installing the software with ‘make check’
Please help in resolving this:
The following tests FAILED:
7 - NbLibSetupTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:71: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:3275: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:3309: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:628: check] Error 2