[gmx-users] Three Regression tests were failed while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.4)

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 14 18:01:32 CET 2018


Hi,

Those look like known issues that we will correct in the 2018.1 patch
release, hopefully out soon. Go ahead and use your installation.

Mark

On Wed, Mar 14, 2018 at 5:07 PM 신동규 <thebiosdk at gmail.com> wrote:

> Hi,
>
> I am trying to install the latest GROMACS on Dell EMC T640(Xeon Gold 6152)
> with Tesla K880 GPU (RHEL 7.4)
>
> AVX-512F related cmake error  was fixed after install devtoolset-6.
>
> cmake command  was:
>
> [root at xxx build] cmake ..  -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON
>
> 3 regression tests(8 - FFTUnitTests (SEGFAULT), 9 - GpuUtilsUnitTests
> (Timeout), 26 - CorrelationsTest (SEGFAULT)) were failed but I don't know
> how to fix it... actually I don't know It should be fix or not.
>
> Any comment or help would be appreciated.
>
> Dongkyu
>
> ----------------------------------------------------------------------
> Output is here..
> .....
> ......
>       Start  1: TestUtilsUnitTests
>  1/39 Test  #1: TestUtilsUnitTests ...............   Passed    0.02 sec
>       Start  2: TestUtilsMpiUnitTests
>  2/39 Test  #2: TestUtilsMpiUnitTests ............   Passed    0.01 sec
>       Start  3: MdlibUnitTest
>  3/39 Test  #3: MdlibUnitTest ....................   Passed    0.01 sec
>       Start  4: AppliedForcesUnitTest
>  4/39 Test  #4: AppliedForcesUnitTest ............   Passed    0.01 sec
>       Start  5: ListedForcesTest
>  5/39 Test  #5: ListedForcesTest .................   Passed    0.01 sec
>       Start  6: CommandLineUnitTests
>  6/39 Test  #6: CommandLineUnitTests .............   Passed    0.01 sec
>       Start  7: EwaldUnitTests
>  7/39 Test  #7: EwaldUnitTests ...................   Passed   13.32 sec
>       Start  8: FFTUnitTests
>  8/39 Test  #8: FFTUnitTests .....................***Exception: SegFault
> 0.06 sec
> [==========] Running 14 tests from 4 test cases.
> [----------] Global test environment set-up.
> [----------] 2 tests from ManyFFTTest
> [ RUN      ] ManyFFTTest.Complex1DLength48Multi5Test
>
>       Start  9: GpuUtilsUnitTests
>  9/39 Test  #9: GpuUtilsUnitTests ................***Timeout  30.70 sec
> [==========] Running 35 tests from 7 test cases.
> [----------] Global test environment set-up.
> [----------] 7 tests from HostAllocatorTest/0, where TypeParam = int
> [ RUN      ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
> [       OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (7472 ms)
> [ RUN      ] HostAllocatorTest/0.VectorsWithDefaultHostAllocatorAlwaysWorks
> [       OK ] HostAllocatorTest/0.VectorsWithDefaultHostAllocatorAlwaysWorks
> (1673 ms)
> [ RUN      ] HostAllocatorTest/0.TransfersWithoutPinningWork
> [       OK ] HostAllocatorTest/0.TransfersWithoutPinningWork (2192 ms)
> [ RUN      ] HostAllocatorTest/0.FillInputAlsoWorksAfterCallingReserve
> [       OK ] HostAllocatorTest/0.FillInputAlsoWorksAfterCallingReserve
> (1217 ms)
> [ RUN      ] HostAllocatorTest/0.TransfersWithPinningWorkWithCuda
> [       OK ] HostAllocatorTest/0.TransfersWithPinningWorkWithCuda (2736 ms)
> [ RUN      ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda
> [       OK ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda (1211
> ms)
> [ RUN      ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
> [       OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (1182 ms)
> [----------] 7 tests from HostAllocatorTest/0 (17683 ms total)
>
> [----------] 7 tests from HostAllocatorTest/1, where TypeParam = float
> [ RUN      ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
> [       OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (1730 ms)
> [ RUN      ] HostAllocatorTest/1.VectorsWithDefaultHostAllocatorAlwaysWorks
> [       OK ] HostAllocatorTest/1.VectorsWithDefaultHostAllocatorAlwaysWorks
> (1681 ms)
> [ RUN      ] HostAllocatorTest/1.TransfersWithoutPinningWork
> [       OK ] HostAllocatorTest/1.TransfersWithoutPinningWork (2223 ms)
> [ RUN      ] HostAllocatorTest/1.FillInputAlsoWorksAfterCallingReserve
> [       OK ] HostAllocatorTest/1.FillInputAlsoWorksAfterCallingReserve
> (1198 ms)
> [ RUN      ] HostAllocatorTest/1.TransfersWithPinningWorkWithCuda
> [       OK ] HostAllocatorTest/1.TransfersWithPinningWorkWithCuda (2669 ms)
> [ RUN      ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda
> [       OK ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda (1223
> ms)
> [ RUN      ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
> [       OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (1194 ms)
> [----------] 7 tests from HostAllocatorTest/1 (11918 ms total)
>
> [----------] 7 tests from HostAllocatorTest/2, where TypeParam =
> gmx::BasicVector<float>
> [ RUN      ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
>
>       Start 10: HardwareUnitTests
> 10/39 Test #10: HardwareUnitTests ................   Passed    0.04 sec
>       Start 11: MathUnitTests
> 11/39 Test #11: MathUnitTests ....................   Passed    0.02 sec
>       Start 12: MdrunUtilityUnitTests
> 12/39 Test #12: MdrunUtilityUnitTests ............   Passed    0.01 sec
>       Start 13: MdrunUtilityMpiUnitTests
> 13/39 Test #13: MdrunUtilityMpiUnitTests .........   Passed    0.02 sec
>       Start 14: OnlineHelpUnitTests
> 14/39 Test #14: OnlineHelpUnitTests ..............   Passed    0.01 sec
>       Start 15: OptionsUnitTests
> 15/39 Test #15: OptionsUnitTests .................   Passed    0.01 sec
>       Start 16: RandomUnitTests
> 16/39 Test #16: RandomUnitTests ..................   Passed    0.02 sec
>       Start 17: TableUnitTests
> 17/39 Test #17: TableUnitTests ...................   Passed    0.22 sec
>       Start 18: TaskAssignmentUnitTests
> 18/39 Test #18: TaskAssignmentUnitTests ..........   Passed    0.01 sec
>       Start 19: UtilityUnitTests
> 19/39 Test #19: UtilityUnitTests .................   Passed    0.02 sec
>       Start 20: FileIOTests
> 20/39 Test #20: FileIOTests ......................   Passed    0.01 sec
>       Start 21: PullTest
> 21/39 Test #21: PullTest .........................   Passed    0.01 sec
>       Start 22: AwhTest
> 22/39 Test #22: AwhTest ..........................   Passed    0.01 sec
>       Start 23: SimdUnitTests
> 23/39 Test #23: SimdUnitTests ....................   Passed    0.06 sec
>       Start 24: GmxAnaTest
> 24/39 Test #24: GmxAnaTest .......................   Passed    0.04 sec
>       Start 25: GmxPreprocessTests
> 25/39 Test #25: GmxPreprocessTests ...............   Passed    0.16 sec
>       Start 26: CorrelationsTest
> 26/39 Test #26: CorrelationsTest .................***Exception: SegFault
> 0.95 sec
> [==========] Running 21 tests from 3 test cases.
> [----------] Global test environment set-up.
> [----------] 10 tests from AutocorrTest
> [ RUN      ] AutocorrTest.EacNormal
> [       OK ] AutocorrTest.EacNormal (117 ms)
> [ RUN      ] AutocorrTest.EacNoNormalize
>
>       Start 27: AnalysisDataUnitTests
> 27/39 Test #27: AnalysisDataUnitTests ............   Passed    0.04 sec
>       Start 28: SelectionUnitTests
> 28/39 Test #28: SelectionUnitTests ...............   Passed    0.11 sec
>       Start 29: TrajectoryAnalysisUnitTests
> 29/39 Test #29: TrajectoryAnalysisUnitTests ......   Passed    0.25 sec
>       Start 30: EnergyAnalysisUnitTests
> 30/39 Test #30: EnergyAnalysisUnitTests ..........   Passed    0.34 sec
>       Start 31: CompatibilityHelpersTests
> 31/39 Test #31: CompatibilityHelpersTests ........   Passed    0.01 sec
>       Start 32: MdrunTests
> 32/39 Test #32: MdrunTests .......................   Passed   97.24 sec
>       Start 33: MdrunMpiTests
> 33/39 Test #33: MdrunMpiTests ....................   Passed    9.60 sec
>       Start 34: regressiontests/simple
> 34/39 Test #34: regressiontests/simple ...........   Passed  134.02 sec
>       Start 35: regressiontests/complex
> 35/39 Test #35: regressiontests/complex ..........   Passed  529.91 sec
>       Start 36: regressiontests/kernel
> 36/39 Test #36: regressiontests/kernel ...........   Passed  1158.78 sec
>       Start 37: regressiontests/freeenergy
> 37/39 Test #37: regressiontests/freeenergy .......   Passed  130.76 sec
>       Start 38: regressiontests/pdb2gmx
> 38/39 Test #38: regressiontests/pdb2gmx ..........   Passed  383.37 sec
>       Start 39: regressiontests/rotation
> 39/39 Test #39: regressiontests/rotation .........   Passed   95.30 sec
>
> 92% tests passed, 3 tests failed out of 39
>
> Label Time Summary:
> GTest              = 153.32 sec*proc (33 tests)
> IntegrationTest    = 106.88 sec*proc (3 tests)
> MpiTest            =   9.63 sec*proc (3 tests)
> UnitTest           =  46.44 sec*proc (30 tests)
>
> Total Test time (real) = 2585.53 sec
>
> The following tests FAILED:
>           8 - FFTUnitTests (SEGFAULT)
>           9 - GpuUtilsUnitTests (Timeout)
>          26 - CorrelationsTest (SEGFAULT)
> Errors while running CTest
> CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> 'CMakeFiles/run-ctest-nophys' failed
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> CMakeFiles/Makefile2:1224: recipe for target
> 'CMakeFiles/run-ctest-nophys.dir/all' failed
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> CMakeFiles/Makefile2:1035: recipe for target 'CMakeFiles/check.dir/rule'
> failed
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> Makefile:574: recipe for target 'check' failed
> make: *** [check] Error 2
>
> ------------------------------------------------------------------------------------------------------------
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