thread-MPI 2021.1 fails some tests, but not MPI version

User discussions
1

GROMACS version: 2021.1
GROMACS modification: No

Hello,

When I compile thread-MPI Gromacs 2021.1 it fails some tests:
$ cmake … -DGMX_GPU=CUDA -DGMX_MPI=OFF -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2021.1 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
…
[----------] Global test environment tear-down
[==========] 10 tests from 1 test case ran. (2520 ms total)
[ PASSED ] 7 tests.
[ FAILED ] 3 tests, listed below:
[ FAILED ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s, where GetParam() = (“relative”, 10, { 87, 89, 90, 91 })
[ FAILED ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s, where GetParam() = (“relative-position-restraints”, 10, { 87, 89, 90, 91, 92 })
[ FAILED ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s, where GetParam() = (“transformAtoB”, 0, { 87 })

3 FAILED TESTS

  Start 65: MdrunSimulatorComparison

65/71 Test #65: MdrunSimulatorComparison … Passed 0.01 sec
Start 66: GmxapiExternalInterfaceTests
66/71 Test #66: GmxapiExternalInterfaceTests … Passed 2.14 sec
Start 67: GmxapiInternalInterfaceTests
67/71 Test #67: GmxapiInternalInterfaceTests … Passed 0.48 sec
Start 68: regressiontests/complex
68/71 Test #68: regressiontests/complex … Passed 50.77 sec
Start 69: regressiontests/freeenergy
69/71 Test #69: regressiontests/freeenergy … Passed 8.50 sec
Start 70: regressiontests/rotation
70/71 Test #70: regressiontests/rotation … Passed 5.13 sec
Start 71: regressiontests/essentialdynamics
71/71 Test #71: regressiontests/essentialdynamics … Passed 3.15 sec

97% tests passed, 2 tests failed out of 71

Label Time Summary:
GTest = 118.67 secproc (65 tests)
IntegrationTest = 43.81 secproc (18 tests)
MpiTest = 70.46 secproc (8 tests)
SlowTest = 72.96 secproc (8 tests)
UnitTest = 1.90 sec*proc (39 tests)

Total Test time (real) = 186.29 sec

The following tests FAILED:
44 - Pdb2gmx3Test (Failed)
64 - MdrunFEPTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:58: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:2755: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2734: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:249: check] Error 2

However, MPI version passed all tests:
$ cmake … -DGMX_GPU=CUDA -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2021.1_mpi -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx

What could be the problem with the thread-MPI version?

Thanks in advance!

Best,
Vasyl

2

I reinstalled cmake, gcc and g++ compilers, and now it fails 1 test:

…
66/71 Test #66: GmxapiExternalInterfaceTests …***Failed 0.02 sec
/home/vasyl/Downloads/gromacs-2021.1/build2/bin/gmxapi-test: symbol lookup error: /home/vasyl/Downloads/gromacs-2021.1/build2/bin/gmxapi-test: undefined symbol: _ZN6gmxapi13createContextEv
…

99% tests passed, 1 tests failed out of 71

Label Time Summary:
GTest = 115.29 secproc (65 tests)
IntegrationTest = 41.28 secproc (18 tests)
MpiTest = 69.94 secproc (8 tests)
SlowTest = 72.28 secproc (8 tests)
UnitTest = 1.73 sec*proc (39 tests)

Total Test time (real) = 184.94 sec

The following tests FAILED:
66 - GmxapiExternalInterfaceTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:58: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:2755: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2734: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:249: check] Error 2

3

Just nosing here, as also have problems installing, but failing other tests (see my post from a few days ago). Still don’t have a solution unfortunately

4

Figured it out. Started new bash window without gromacs 2021 environment and now it passed 100% tests.