[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)
신동규
thebiosdk at gmail.com
Thu Mar 15 05:10:15 CET 2018
Hi Mark,
Thank you for your kind comment.
Dongkyu
2018-03-15 2:01 GMT+09:00 Mark Abraham <mark.j.abraham at gmail.com>:
> 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.VectorsWithDefaultHostAllocato
> rAlwaysWorks
> > [ OK ] HostAllocatorTest/0.VectorsWithDefaultHostAllocato
> rAlwaysWorks
> > (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.VectorsWithDefaultHostAllocato
> rAlwaysWorks
> > [ OK ] HostAllocatorTest/1.VectorsWithDefaultHostAllocato
> rAlwaysWorks
> > (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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