[gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4)

[Adam Antoszewski]

Hey all,

I am trying to install GROMACS 2019.4 (patched with plumed 2.5.3)  on the
Bridges <https://portal.xsede.org/psc-bridges> cluster, which uses Intel
Haswell CPUS. When compiling/installing with GNU compiler (GCC 4.8.4) and
OpenMPI, the compile runs well. The cmake command I used was :

cmake .. \

    -DCMAKE_C_COMPILER=mpicc \

    -DCMAKE_CXX_COMPILER=mpicxx \

    -DGMX_MPI=ON \

    -DCMAKE_INSTALL_PREFIX="${INSTALL_ROOT}" \

    -DGMX_BUILD_OWN_FFTW=OFF \

    -DGMX_FFT_LIBRARY=fftw3 \

    -DREGRESSIONTEST_PATH="${BUILD_ROOT}/regressiontests-2019.4" \
    -DGMX_SIMD=AVX2_256

Upon running 'make check', I pass 47/48 tests. The only test I fail is the
HardwareUnitTests, specifically the HardwareTopologyTest. The error message
I receive is reproduced below.

-------

11/46 Test #11: HardwareUnitTests ...................***Failed    0.65 sec

[==========] Running 5 tests from 2 test cases.

[----------] Global test environment set-up.

[----------] 1 test from CpuInfoTest

[ RUN      ] CpuInfoTest.SupportLevel

[       OK ] CpuInfoTest.SupportLevel (1 ms)

[----------] 1 test from CpuInfoTest (1 ms total)


[----------] 4 tests from HardwareTopologyTest

[ RUN      ] HardwareTopologyTest.Execute

[       OK ] HardwareTopologyTest.Execute (57 ms)

[ RUN      ] HardwareTopologyTest.HwlocExecute

/pylon5/mc5fphp/anto/gromacs_src/gromacs-2019.4/src/gromacs/hardware/tests/hardwaretopology.cpp:88:
Failure

Expected: (hwTop.supportLevel()) >=
(gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00
00-00> vs 4-byte object <02-00 00-00>

Cannot determine basic hardware topology from hwloc. GROMACS will still


work, but it might affect your performance for large nodes.

Please mail gmx-developers at gromacs.org so we can try to fix it.

[  FAILED  ] HardwareTopologyTest.HwlocExecute (51 ms)

[ RUN      ] HardwareTopologyTest.ProcessorSelfconsistency

[       OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms)

[ RUN      ] HardwareTopologyTest.NumaCacheSelfconsistency

[       OK ] HardwareTopologyTest.NumaCacheSelfconsistency (48 ms)

[----------] 4 tests from HardwareTopologyTest (206 ms total)


[----------] Global test environment tear-down

[==========] 5 tests from 2 test cases ran. (207 ms total)

[  PASSED  ] 4 tests.

[  FAILED  ] 1 test, listed below:

[  FAILED  ] HardwareTopologyTest.HwlocExecute


 1 FAILED TEST


.

.

.


98% tests passed, 1 tests failed out of 46


Label Time Summary:

GTest              = 137.68 sec (40 tests)

IntegrationTest    = 103.21 sec (5 tests)

MpiTest            =   1.36 sec (3 tests)

SlowTest           =  15.28 sec (1 test)

UnitTest           =  19.18 sec (34 tests)


Total Test time (real) = 1461.58 sec


The following tests FAILED:

11 - HardwareUnitTests (Failed)

Errors while running CTest

make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8

make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2

make[1]: *** [CMakeFiles/check
--------

The rest of the tests pass without issue, so . Any ideas? Is this some
issue with hwloc, and is there anything I can do to fix it, or do I need to
contact the sys admins? Is this a big issue, even with the failed test? The
nodes only ever have 24 CPUs, so I'm not sure if that counts as a 'large
node' (or if the number of nodes used per simulation would matter). Thanks
in advance for the help! By the way, I am emailing this list because the
error message told me to email gmx-developers, but I don't have permissions
to post there - I apologize if this is the wrong forum.

Thanks so much!

-- 
Adam Antoszewski, PhD Candidate
Dept. of Chemistry, The University of Chicago
antoszewski at uchicago.edu