[gmx-users] Make check failed 2018 Gromacs on GPU workstation

[Szilárd Páll]

Test timeouts are strange, Is the machine you're running on busy with other
jobs?

Regarding the regressiontest failure, can you share
tests/regressiontests*/complex/octahedron/mdrun.out
please?

--
Szilárd


On Thu, Sep 13, 2018 at 8:49 PM Phuong Tran <tranphuonguns at gmail.com> wrote:

> Hi all,
>
> I have been trying to install Gromacs on our GPU workstation that has CUDA
> 9.0
> It went well but 'make check' have failed so far on either 2018.3 or 2018.2
> versions.
> anybody know how to resolve it?
> Please see the error below.
> Thank you,
> -T
>
> Test project /home/user/Softwares/gromacs-2018.3/build
>
> .....
>
>
>  9/39 Test  #9: GpuUtilsUnitTests ................***Timeout  30.35 sec
>
>
> .....
>
>
> 35/39 Test #35: regressiontests/complex ..........***Failed  174.98 sec
>
>
>
> GROMACS:      gmx mdrun, version 2018.3
>
> Executable:   /home/user/Softwares/gromacs-2018.3/build/bin/gmx
>
> Data prefix:  /home/user/Softwares/gromacs-2018.3 (source tree)
>
> Working dir:
> /home/user/Softwares/gromacs-2018.3/build/tests/regressiontests-2018.3
>
> Command line:
>
>   gmx mdrun -h
>
>
>
> Thanx for Using GROMACS - Have a Nice Day
>
>
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
>
>
> Abnormal return value for ' gmx mdrun    -nb cpu   -notunepme >mdrun.out
> 2>&1' was 1
>
> Retrying mdrun with better settings...
>
>
> Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was
> -1
>
> FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
>
> Re-running orientation-restraints using CPU-based PME
>
> Re-running pull_geometry_angle using CPU-based PME
>
> Re-running pull_geometry_angle-axis using CPU-based PME
>
> Re-running pull_geometry_dihedral using CPU-based PME
>
> 1 out of 55 complex tests FAILED
>
>
>  ....
>
>
> 95% tests passed, 2 tests failed out of 39
>
>
> Label Time Summary:
>
> GTest              = 133.55 sec (33 tests)
>
> IntegrationTest    =  88.38 sec (3 tests)
>
> MpiTest            =   2.82 sec (3 tests)
>
> UnitTest           =  45.17 sec (30 tests)
>
>
> Total Test time (real) = 810.78 sec
>
>
> The following tests FAILED:
>
>   9 - GpuUtilsUnitTests (Timeout)
>
>  35 - regressiontests/complex (Failed)
>
> 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/Makefile2:1160: recipe for target
> 'CMakeFiles/run-ctest-nophys.dir/all' failed
>
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
>
> CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
> failed
>
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
>
> Makefile:546: recipe for target 'check' failed
>
> make: *** [check] Error 2
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