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-develop...@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
antoszew...@uchicago.edu
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