GROMACS version: 2021.2
GROMACS modification: No
Greetings.
I have successfully installed gromacs 2021.2 in my machine (ubuntu 20.04).
However, when I try to do it with gpu support, using the cuda flags in the cmake
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA
four tests during make check fail:
12 - MdlibUnitTest (Failed)
19 - DomDecMpiTests (Failed)
20 - EwaldUnitTests (Failed)
22 - GpuUtilsUnitTests (Failed)
I have two GPUS, GeForce RTX 2080 , cuda 11.3.
Is there something I have to consider with this setup?
I attach the nvidia-smi and make check outputs below.
Many thanks in advance.
Simón.
The nvidia-smi output:
±----------------------------------------------------------------------------+
| NVIDIA-SMI 465.19.01 Driver Version: 465.19.01 CUDA Version: 11.3 |
|-------------------------------±---------------------±---------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 NVIDIA GeForce … On | 00000000:0A:00.0 Off | N/A |
| 0% 25C P8 19W / 250W | 15MiB / 7982MiB | 0% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
| 1 NVIDIA GeForce … On | 00000000:42:00.0 Off | N/A |
| 0% 27C P8 11W / 250W | 756MiB / 7979MiB | 0% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
±----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 1451 G /usr/lib/xorg/Xorg 4MiB |
| 0 N/A N/A 55502 G /usr/lib/xorg/Xorg 4MiB |
| 0 N/A N/A 56754 G /usr/lib/xorg/Xorg 4MiB |
| 1 N/A N/A 1451 G /usr/lib/xorg/Xorg 102MiB |
| 1 N/A N/A 55502 G /usr/lib/xorg/Xorg 111MiB |
| 1 N/A N/A 56036 G /usr/lib/firefox/firefox 189MiB |
| 1 N/A N/A 56754 G /usr/lib/xorg/Xorg 182MiB |
| 1 N/A N/A 56881 G /usr/bin/gnome-shell 10MiB |
±----------------------------------------------------------------------------+
The output of the make check is
– The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;–enable-avx;–enable-avx2
– Configuring done
– Generating done
– Build files have been written to: /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build
…
Test project /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build
Start 1: NbLibListedForcesTests
1/71 Test #1: NbLibListedForcesTests … Passed 0.01 sec
Start 2: NbLibSamplesTestArgon
2/71 Test #2: NbLibSamplesTestArgon … Passed 0.00 sec
Start 3: NbLibSamplesTestMethaneWater
3/71 Test #3: NbLibSamplesTestMethaneWater … Passed 0.01 sec
Start 4: NbLibUtilTests
4/71 Test #4: NbLibUtilTests … Passed 0.01 sec
Start 5: NbLibSetupTests
5/71 Test #5: NbLibSetupTests … Passed 0.01 sec
Start 6: NbLibIntegrationTests
6/71 Test #6: NbLibIntegrationTests … Passed 0.01 sec
Start 7: NbLibIntegratorTests
7/71 Test #7: NbLibIntegratorTests … Passed 0.00 sec
Start 8: TestUtilsUnitTests
8/71 Test #8: TestUtilsUnitTests … Passed 0.01 sec
Start 9: TestUtilsMpiUnitTests
9/71 Test #9: TestUtilsMpiUnitTests … Passed 0.00 sec
Start 10: UtilityUnitTests
10/71 Test #10: UtilityUnitTests … Passed 0.02 sec
Start 11: UtilityMpiUnitTests
11/71 Test #11: UtilityMpiUnitTests … Passed 0.01 sec
Start 12: MdlibUnitTest
12/71 Test #12: MdlibUnitTest …***Failed 0.00 sec
/home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/mdlib-test: symbol lookup error: /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/mdlib-test: undefined symbol: _ZN3gmx11LeapFrogGpuC1ERK13DeviceContextRK12DeviceStream
Start 13: AwhTest
13/71 Test #13: AwhTest … Passed 0.03 sec
Start 14: DensityFittingAppliedForcesUnitTest
14/71 Test #14: DensityFittingAppliedForcesUnitTest … Passed 0.01 sec
Start 15: AppliedForcesUnitTest
15/71 Test #15: AppliedForcesUnitTest … Passed 0.01 sec
Start 16: ListedForcesTest
16/71 Test #16: ListedForcesTest … Passed 0.02 sec
Start 17: CommandLineUnitTests
17/71 Test #17: CommandLineUnitTests … Passed 0.01 sec
Start 18: DomDecTests
18/71 Test #18: DomDecTests … Passed 0.01 sec
Start 19: DomDecMpiTests
19/71 Test #19: DomDecMpiTests …***Failed 0.00 sec
/home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/domdec-mpi-test: symbol lookup error: /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/domdec-mpi-test: undefined symbol: _ZNK12DeviceStream6streamEv
Start 20: EwaldUnitTests
20/71 Test #20: EwaldUnitTests …***Failed 0.00 sec
/home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/ewald-test: symbol lookup error: /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/ewald-test: undefined symbol: _Z14pme_gpu_spreadPK6PmeGpuP20GpuEventSynchronizerPPfbbf
Start 21: FFTUnitTests
21/71 Test #21: FFTUnitTests … Passed 0.05 sec
Start 22: GpuUtilsUnitTests
22/71 Test #22: GpuUtilsUnitTests …***Failed 0.00 sec
/home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/gpu_utils-test: symbol lookup error: /home/spoblete/Applications/gromacs/gromacs-2021.2-cuda/gromacs-2021.2/build/bin/gpu_utils-test: undefined symbol: _ZNK12DeviceStream6streamEv
Start 23: HardwareUnitTests
23/71 Test #23: HardwareUnitTests … Passed 0.01 sec
Start 24: MathUnitTests
24/71 Test #24: MathUnitTests … Passed 0.05 sec
Start 25: MdrunUtilityUnitTests
25/71 Test #25: MdrunUtilityUnitTests … Passed 0.01 sec
Start 26: MdrunUtilityMpiUnitTests
26/71 Test #26: MdrunUtilityMpiUnitTests … Passed 0.01 sec
Start 27: MDSpanTests
27/71 Test #27: MDSpanTests … Passed 0.01 sec
Start 28: MdtypesUnitTest
28/71 Test #28: MdtypesUnitTest … Passed 0.01 sec
Start 29: OnlineHelpUnitTests
29/71 Test #29: OnlineHelpUnitTests … Passed 0.00 sec
Start 30: OptionsUnitTests
30/71 Test #30: OptionsUnitTests … Passed 0.01 sec
Start 31: PbcutilUnitTest
31/71 Test #31: PbcutilUnitTest … Passed 0.01 sec
Start 32: RandomUnitTests
32/71 Test #32: RandomUnitTests … Passed 0.01 sec
Start 33: RestraintTests
33/71 Test #33: RestraintTests … Passed 0.00 sec
Start 34: TableUnitTests
34/71 Test #34: TableUnitTests … Passed 0.04 sec
Start 35: TaskAssignmentUnitTests
35/71 Test #35: TaskAssignmentUnitTests … Passed 0.00 sec
Start 36: TopologyTest
36/71 Test #36: TopologyTest … Passed 0.00 sec
Start 37: PullTest
37/71 Test #37: PullTest … Passed 0.00 sec
Start 38: SimdUnitTests
38/71 Test #38: SimdUnitTests … Passed 0.02 sec
Start 39: CompatibilityHelpersTests
39/71 Test #39: CompatibilityHelpersTests … Passed 0.00 sec
Start 40: GmxAnaTest
40/71 Test #40: GmxAnaTest … Passed 0.59 sec
Start 41: GmxPreprocessTests
41/71 Test #41: GmxPreprocessTests … Passed 0.61 sec
Start 42: Pdb2gmx1Test
42/71 Test #42: Pdb2gmx1Test … Passed 0.85 sec
Start 43: Pdb2gmx2Test
43/71 Test #43: Pdb2gmx2Test … Passed 0.74 sec
Start 44: Pdb2gmx3Test
44/71 Test #44: Pdb2gmx3Test … Passed 8.01 sec
Start 45: CorrelationsTest
45/71 Test #45: CorrelationsTest … Passed 0.53 sec
Start 46: AnalysisDataUnitTests
46/71 Test #46: AnalysisDataUnitTests … Passed 0.02 sec
Start 47: CoordinateIOTests
47/71 Test #47: CoordinateIOTests … Passed 0.07 sec
Start 48: TrajectoryAnalysisUnitTests
48/71 Test #48: TrajectoryAnalysisUnitTests … Passed 0.48 sec
Start 49: EnergyAnalysisUnitTests
49/71 Test #49: EnergyAnalysisUnitTests … Passed 0.11 sec
Start 50: ToolUnitTests
50/71 Test #50: ToolUnitTests … Passed 0.47 sec
Start 51: FileIOTests
51/71 Test #51: FileIOTests … Passed 0.01 sec
Start 52: SelectionUnitTests
52/71 Test #52: SelectionUnitTests … Passed 0.08 sec
Start 53: MdrunOutputTests
53/71 Test #53: MdrunOutputTests … Passed 0.16 sec
Start 54: MdrunModulesTests
54/71 Test #54: MdrunModulesTests … Passed 0.20 sec
Start 55: MdrunIOTests
55/71 Test #55: MdrunIOTests … Passed 2.26 sec
Start 56: MdrunTests
56/71 Test #56: MdrunTests … Passed 1.73 sec
Start 57: MdrunPmeTests
57/71 Test #57: MdrunPmeTests … Passed 0.62 sec
Start 58: MdrunNonIntegratorTests
58/71 Test #58: MdrunNonIntegratorTests … Passed 2.77 sec
Start 59: MdrunTpiTests
59/71 Test #59: MdrunTpiTests … Passed 0.42 sec
Start 60: MdrunMpiTests
60/71 Test #60: MdrunMpiTests … Passed 1.31 sec
Start 61: MdrunMpiPmeTests
61/71 Test #61: MdrunMpiPmeTests … Passed 0.61 sec
Start 62: MdrunMpiCoordinationTestsOneRank
62/71 Test #62: MdrunMpiCoordinationTestsOneRank … Passed 18.34 sec
Start 63: MdrunMpiCoordinationTestsTwoRanks
63/71 Test #63: MdrunMpiCoordinationTestsTwoRanks … Passed 19.03 sec
Start 64: MdrunFEPTests
64/71 Test #64: MdrunFEPTests … Passed 0.71 sec
Start 65: MdrunSimulatorComparison
65/71 Test #65: MdrunSimulatorComparison … Passed 0.01 sec
Start 66: GmxapiExternalInterfaceTests
66/71 Test #66: GmxapiExternalInterfaceTests … Passed 1.36 sec
Start 67: GmxapiInternalInterfaceTests
67/71 Test #67: GmxapiInternalInterfaceTests … Passed 0.42 sec
Start 68: regressiontests/complex
68/71 Test #68: regressiontests/complex … Passed 59.71 sec
Start 69: regressiontests/freeenergy
69/71 Test #69: regressiontests/freeenergy … Passed 39.62 sec
Start 70: regressiontests/rotation
70/71 Test #70: regressiontests/rotation … Passed 3.14 sec
Start 71: regressiontests/essentialdynamics
71/71 Test #71: regressiontests/essentialdynamics … Passed 7.17 sec
94% tests passed, 4 tests failed out of 71
Label Time Summary:
GTest = 62.96 secproc (65 tests)
IntegrationTest = 13.20 secproc (18 tests)
MpiTest = 39.33 secproc (8 tests)
SlowTest = 48.54 secproc (8 tests)
UnitTest = 1.22 sec*proc (39 tests)
Total Test time (real) = 172.65 sec
The following tests FAILED:
12 - MdlibUnitTest (Failed)
19 - DomDecMpiTests (Failed)
20 - EwaldUnitTests (Failed)
22 - GpuUtilsUnitTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:58: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:2738: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2717: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:249: check] Error 2