Gromacs 2018.4 install make check failed

User discussions
1

GROMACS version: 2018.4
GROMACS modification: NO

Hello!
I got a fail when i executed “make check” in the compilation process.
Firstly i introduce my configuration environment:
System: Centos 7.8
CPU: Intel(R) Xeon(R) Gold 5218R
GPU: Tesla V100s
Driver Version: 460.73.01 CUDA Version: 11.2

Then i introduce the protocol of compilation:

  1. cmake … -DGMX_CUDA_TARGET_COMPUTE=70 -DCMAKE_PREFIX_PATH=/data/yiming-wangshuai/software/fftw-3.3.10/install-enableshare/bin -DCMAKE_LIBRARY_PATH=/data/yiming-wangshuai/software/fftw-3.3.10/install-enableshare/lib -DFFTWF_INCLUDE_DIR=/data/yiming-wangshuai/software/fftw-3.3.10/install-enableshare/include -DGMX_BUILD_OWN_FFTW=OFF -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/data/yiming-wangshuai/software/gromacs-2018.4/install-gcc5.4-avx2_256-cuda11.2-master -DCUDA_TOOLKIT_ROOT_DIR=/data/yiming-wangshuai/software/cuda-11.2 -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=OFF -DGMX_EXTERNAL_TNG=OFF -DGMX_SIMD=AVX2_256 -DCMAKE_CXX_COMPILER=/usr/local/gcc-5.4.0/bin/c++ -DFFTW_LIBRARY=/data/yiming-wangshuai/software/fftw-3.3.10/install-enableshare/lib/libfftw3f.so
  2. make -j 40
  3. make check
    In this step, i got a fail. I copy the information of fail bellow.
    …
    [100%] Running all tests except physical validation
    Test project /data/yiming-wangshuai/software/gromacs-2018.4/build-gcc5.4-avx2_256-cuda11.2-master
    Start 1: TestUtilsUnitTests
    1/33 Test #1: TestUtilsUnitTests … Passed 0.15 sec
    Start 2: TestUtilsMpiUnitTests
    2/33 Test #2: TestUtilsMpiUnitTests … Passed 0.05 sec
    Start 3: MdlibUnitTest
    3/33 Test #3: MdlibUnitTest … Passed 0.07 sec
    Start 4: AppliedForcesUnitTest
    4/33 Test #4: AppliedForcesUnitTest … Passed 0.06 sec
    Start 5: ListedForcesTest
    5/33 Test #5: ListedForcesTest … Passed 0.07 sec
    Start 6: CommandLineUnitTests
    6/33 Test #6: CommandLineUnitTests … Passed 0.10 sec
    Start 7: EwaldUnitTests
    7/33 Test #7: EwaldUnitTests … Passed 5.87 sec
    Start 8: FFTUnitTests
    8/33 Test #8: FFTUnitTests … Passed 0.10 sec
    Start 9: GpuUtilsUnitTests
    9/33 Test #9: GpuUtilsUnitTests …***Failed 23.10 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 (897 ms)
    [ RUN ] HostAllocatorTest/0.VectorsWithDefaultHostAllocatorAlwaysWorks
    [ OK ] HostAllocatorTest/0.VectorsWithDefaultHostAllocatorAlwaysWorks (1079 ms)
    [ RUN ] HostAllocatorTest/0.TransfersWithoutPinningWork
    [ OK ] HostAllocatorTest/0.TransfersWithoutPinningWork (989 ms)
    [ RUN ] HostAllocatorTest/0.FillInputAlsoWorksAfterCallingReserve
    [ OK ] HostAllocatorTest/0.FillInputAlsoWorksAfterCallingReserve (382 ms)
    [ RUN ] HostAllocatorTest/0.TransfersWithPinningWorkWithCuda
    [ OK ] HostAllocatorTest/0.TransfersWithPinningWorkWithCuda (2729 ms)
    [ RUN ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda
    /data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:277: Failure
    Value of: isPinned(input)
    Actual: true
    Expected: false
    /data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:294: Failure
    Value of: isPinned(input)
    Actual: true
    Expected: false
    [ FAILED ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda, where TypeParam = int (653 ms)
    [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
    [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (391 ms)
    [----------] 7 tests from HostAllocatorTest/0 (7122 ms total)

[----------] 7 tests from HostAllocatorTest/1, where TypeParam = float
[ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
[ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (820 ms)
[ RUN ] HostAllocatorTest/1.VectorsWithDefaultHostAllocatorAlwaysWorks
[ OK ] HostAllocatorTest/1.VectorsWithDefaultHostAllocatorAlwaysWorks (680 ms)
[ RUN ] HostAllocatorTest/1.TransfersWithoutPinningWork
[ OK ] HostAllocatorTest/1.TransfersWithoutPinningWork (1267 ms)
[ RUN ] HostAllocatorTest/1.FillInputAlsoWorksAfterCallingReserve
[ OK ] HostAllocatorTest/1.FillInputAlsoWorksAfterCallingReserve (515 ms)
[ RUN ] HostAllocatorTest/1.TransfersWithPinningWorkWithCuda
[ OK ] HostAllocatorTest/1.TransfersWithPinningWorkWithCuda (1655 ms)
[ RUN ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda
/data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:277: Failure
Value of: isPinned(input)
Actual: true
Expected: false
/data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:294: Failure
Value of: isPinned(input)
Actual: true
Expected: false
[ FAILED ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda, where TypeParam = float (383 ms)
[ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
[ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (459 ms)
[----------] 7 tests from HostAllocatorTest/1 (5780 ms total)

[----------] 7 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector
[ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
[ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (830 ms)
[ RUN ] HostAllocatorTest/2.VectorsWithDefaultHostAllocatorAlwaysWorks
[ OK ] HostAllocatorTest/2.VectorsWithDefaultHostAllocatorAlwaysWorks (810 ms)
[ RUN ] HostAllocatorTest/2.TransfersWithoutPinningWork
[ OK ] HostAllocatorTest/2.TransfersWithoutPinningWork (979 ms)
[ RUN ] HostAllocatorTest/2.FillInputAlsoWorksAfterCallingReserve
[ OK ] HostAllocatorTest/2.FillInputAlsoWorksAfterCallingReserve (383 ms)
[ RUN ] HostAllocatorTest/2.TransfersWithPinningWorkWithCuda
[ OK ] HostAllocatorTest/2.TransfersWithPinningWorkWithCuda (1492 ms)
[ RUN ] HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda
/data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:277: Failure
Value of: isPinned(input)
Actual: true
Expected: false
/data/yiming-wangshuai/software/gromacs-2018.4/src/gromacs/gpu_utils/tests/hostallocator.cpp:294: Failure
Value of: isPinned(input)
Actual: true
Expected: false
[ FAILED ] HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda, where TypeParam = gmx::BasicVector (463 ms)
[ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
[ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (426 ms)
[----------] 7 tests from HostAllocatorTest/2 (5383 ms total)

[----------] 3 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
[ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
[ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
[ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
[ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
[ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
[ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
[----------] 3 tests from AllocatorTest/0 (0 ms total)

[----------] 3 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
[ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
[ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
[ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
[ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
[ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
[ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
[----------] 3 tests from AllocatorTest/1 (0 ms total)

[----------] 3 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector, gmx::HostAllocationPolicy>
[ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
[ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
[ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
[ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
[ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
[ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
[----------] 3 tests from AllocatorTest/2 (0 ms total)

[----------] 5 tests from PinnedMemoryCheckerTest
[ RUN ] PinnedMemoryCheckerTest.DefaultContainerIsRecognized
[ OK ] PinnedMemoryCheckerTest.DefaultContainerIsRecognized (827 ms)
[ RUN ] PinnedMemoryCheckerTest.NonpinnedContainerIsRecognized
[ OK ] PinnedMemoryCheckerTest.NonpinnedContainerIsRecognized (678 ms)
[ RUN ] PinnedMemoryCheckerTest.PinnedContainerIsRecognized
[ OK ] PinnedMemoryCheckerTest.PinnedContainerIsRecognized (1322 ms)
[ RUN ] PinnedMemoryCheckerTest.DefaultCBufferIsRecognized
[ OK ] PinnedMemoryCheckerTest.DefaultCBufferIsRecognized (573 ms)
[ RUN ] PinnedMemoryCheckerTest.PinnedCBufferIsRecognized
[ OK ] PinnedMemoryCheckerTest.PinnedCBufferIsRecognized (1239 ms)
[----------] 5 tests from PinnedMemoryCheckerTest (4639 ms total)

[----------] Global test environment tear-down
[==========] 35 tests from 7 test cases ran. (22924 ms total)
[ PASSED ] 32 tests.
[ FAILED ] 3 tests, listed below:
[ FAILED ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda, where TypeParam = int
[ FAILED ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda, where TypeParam = float
[ FAILED ] HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda, where TypeParam = gmx::BasicVector

3 FAILED TESTS

  Start 10: HardwareUnitTests

10/33 Test #10: HardwareUnitTests … Passed 0.29 sec
Start 11: MathUnitTests
11/33 Test #11: MathUnitTests … Passed 0.07 sec
Start 12: MdrunUtilityUnitTests
12/33 Test #12: MdrunUtilityUnitTests … Passed 0.06 sec
Start 13: MdrunUtilityMpiUnitTests
13/33 Test #13: MdrunUtilityMpiUnitTests … Passed 0.07 sec
Start 14: OnlineHelpUnitTests
14/33 Test #14: OnlineHelpUnitTests … Passed 0.05 sec
Start 15: OptionsUnitTests
15/33 Test #15: OptionsUnitTests … Passed 0.05 sec
Start 16: RandomUnitTests
16/33 Test #16: RandomUnitTests … Passed 0.08 sec
Start 17: TableUnitTests
17/33 Test #17: TableUnitTests … Passed 0.24 sec
Start 18: TaskAssignmentUnitTests
18/33 Test #18: TaskAssignmentUnitTests … Passed 0.03 sec
Start 19: UtilityUnitTests
19/33 Test #19: UtilityUnitTests … Passed 0.06 sec
Start 20: FileIOTests
20/33 Test #20: FileIOTests … Passed 0.05 sec
Start 21: PullTest
21/33 Test #21: PullTest … Passed 0.03 sec
Start 22: AwhTest
22/33 Test #22: AwhTest … Passed 0.06 sec
Start 23: SimdUnitTests
23/33 Test #23: SimdUnitTests … Passed 0.09 sec
Start 24: GmxAnaTest
24/33 Test #24: GmxAnaTest … Passed 0.14 sec
Start 25: GmxPreprocessTests
25/33 Test #25: GmxPreprocessTests … Passed 0.52 sec
Start 26: CorrelationsTest
26/33 Test #26: CorrelationsTest … Passed 0.94 sec
Start 27: AnalysisDataUnitTests
27/33 Test #27: AnalysisDataUnitTests … Passed 0.08 sec
Start 28: SelectionUnitTests
28/33 Test #28: SelectionUnitTests … Passed 0.18 sec
Start 29: TrajectoryAnalysisUnitTests
29/33 Test #29: TrajectoryAnalysisUnitTests … Passed 0.51 sec
Start 30: EnergyAnalysisUnitTests
30/33 Test #30: EnergyAnalysisUnitTests … Passed 0.28 sec
Start 31: CompatibilityHelpersTests
31/33 Test #31: CompatibilityHelpersTests … Passed 0.03 sec
Start 32: MdrunTests
^Cmake[3]: *** [CMakeFiles/run-ctest-nophys] Interrupt
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Interrupt
make[1]: *** [CMakeFiles/check.dir/rule] Interrupt
make: *** [check] Interrupt

Much appreciate if anyone can help me.

2

Things that you should check for sure:

  1. Update/install gcc latest version.
  2. Update/install cmake latest version.
  3. Check that your CUDA is installed properly
    (CUDA 9.0 installation in Ubuntu 16.4 + / Linux Mint - Full instruction with verification - YouTube 5:35 here is how to do that)

It might be a problem with CUDA because these lines point to it
[ FAILED ] 3 tests, listed below:
[ FAILED ] HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda, where TypeParam = int
[ FAILED ] HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda, where TypeParam = float
[ FAILED ] HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda, where TypeParam =

You can also check to install a newer version of GROMACS, because for example, it is impossible right now to install a very old version of GROMACS on a new computer with CUDA 11. For example, I can’t install Gromacs 2018.4 on my computer with CUDA 11.7 and GTX 3080 TI (maybe its possible with a lower version of CUDA)

3

Thanks a lot for your suggestions. I solve this problem by downgrade the CUDA version from 11.2 to 10.2.