Gromacs 2022.1 installation, Mdrun Mpi Coordination Constraints test failed for make check

User discussions
1

I’m trying to download GROMACS 2022.1 on my Windows machine using Windows Subsystem for Linux. I’m wondering if the test I’m failing is because my machine isn’t powerful enough. I fail two tests when running make check.

My system specs are an AMD Ryzen 5 5600H CPU with 6 cores, 16GB RAM, and an RTX3060 GPU.

My cmake flags are cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON

These are the failed tests:

[ FAILED ] 2 tests, listed below:
[ FAILED ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9, where GetParam() = ({ (“comm-mode”, “linear”), (“integrator”, “md-vv”), (“maxGromppWarningsTolerated”, “0”), (“nstcomm”, “5”), (“nstpcouple”, “3”), (“nsttcouple”, “2”), (“pcoupl”, “no”), (“simulationName”, “tip3p5”), (“tcoupl”, “no”) }, 0x560ce6437890)
[ FAILED ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10, where GetParam() = ({ (“comm-mode”, “linear”), (“integrator”, “md-vv”), (“maxGromppWarningsTolerated”, “0”), (“nstcomm”, “5”), (“nstpcouple”, “3”), (“nsttcouple”, “2”), (“pcoupl”, “C-rescale”), (“simulationName”, “tip3p5”), (“tcoupl”, “no”) }, 0x560ce6437890)

2 FAILED TESTS

  Start 81: MdrunFEPTests

81/84 Test #81: MdrunFEPTests … Passed 1.06 sec
Start 82: MdrunPullTests
82/84 Test #82: MdrunPullTests … Passed 1.13 sec
Start 83: MdrunSimulatorComparison
83/84 Test #83: MdrunSimulatorComparison … Passed 0.04 sec
Start 84: MdrunVirtualSiteTests
84/84 Test #84: MdrunVirtualSiteTests … Passed 0.70 sec

99% tests passed, 1 tests failed out of 84

Label Time Summary:
GTest = 79.14 secproc (81 tests)
IntegrationTest = 24.38 secproc (25 tests)
MpiTest = 48.46 secproc (19 tests)
SlowTest = 51.53 secproc (13 tests)
UnitTest = 3.23 sec*proc (43 tests)

Total Test time (real) = 79.41 sec

The following tests FAILED:
80 - MdrunMpiCoordinationConstraintsTestsTwoRanks (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:58: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:2804: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2784: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:249: check] Error 2

Anyone know what might be causing this? Thanks!

2

Hello!

We have several similar reports of such issues with GCC and AMD Zen 2 CPUs which we are still investigating.

Are you using GCC compiler? You can try using Clang or setting -DGMX_SIMD=SSE4.1. The latter will impair CPU performance somewhat.

3

This worked, thank you!

4

I had the same or similar issue, and this is what worked for me. My hardware was:

Vendor: Intel
Brand: Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
Family: 6 Model: 79 Stepping: 1
Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
Hardware topology: Basic
Packages, cores, and logical processors:
[indices refer to OS logical processors]
Package 0: [ 0 20] [ 1 21] [ 2 22] [ 3 23] [ 4 24] [ 5 25] [ 6 26] [ 7 27] [ 8 28] [ 9 29]
Package 1: [ 10 30] [ 11 31] [ 12 32] [ 13 33] [ 14 34] [ 15 35] [ 16 36] [ 17 37] [ 18 38] [ 19 39]
CPU limit set by OS: -1 Recommended max number of threads: 40
GPU info:
Number of GPUs detected: 1
#0: NVIDIA NVIDIA GeForce RTX 3080, compute cap.: 8.6, ECC: no, stat: compatible

The issue appears to be in the cmake section and what flags you will use. For me, this did not work using the standard suggested build command, but did with an added flag (shown below):

full standard and suggested build:
tar xfz
gromacs-2022.4.tar.gz
cd
gromacs-2022.4
mkdir build
cd build
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA
make
make check
sudo make install

2 or more test failed when using the standard build (Some test failing):
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA

Worked like this (All test passing tests):
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_CXX_COMPILER=/usr/bin/g++