[gmx-users] Make check failed 2018 Gromacs on GPU workstation
Szilárd Páll
pall.szilard at gmail.com
Tue Sep 18 12:48:49 CEST 2018
Thanks, that looks like the an issue with the tests not picking the right
run configuration for the hardware. Can you please file a report on
redmine.gromacs.org.
You can make sure that otherwise the tests pass by restricting the testing
to e.g. a single GPU using CUDA_VISIBLE_DEVICES=0.
--
Szilárd
On Fri, Sep 14, 2018 at 10:54 PM Phuong Tran <tranphuonguns at gmail.com>
wrote:
> Thank you for your quick response.
>
> I have no idea why the GPU unit test failed. The workstation was restarted,
> so nothing was running at the time. We have 1 Quadro 600, and 2 1080Ti on
> it with CUDA 9.0.
> Here is the result for the regression test:
>
> Reading file topol.tpr, VERSION 2018.3 (single precision)
>
> NOTE: Parallelization is limited by the small number of atoms,
> only starting 4 thread-MPI ranks.
> You can use the -nt and/or -ntmpi option to optimize the number of
> threads.
>
> Changing nstlist from 10 to 100, rlist from 1.4 to 1.536
>
> Using 4 MPI threads
> Using 8 OpenMP threads per tMPI thread
>
>
> -------------------------------------------------------
> Program: gmx mdrun, version 2018.3
> Source file: src/gromacs/taskassignment/taskassignment.cpp (line 251)
> Function: std::vector<std::vector<gmx::GpuTaskMapping> >::value_type
> gmx::runTaskAssignment(const std::vector<int>&, const std::vector<int>&,
> const gmx_hw_info_t&, const gmx::MDLogger&, const t_commrec*, const
> std::vector<gmx::GpuTask>&)
> MPI rank: 0 (out of 4)
>
> Inconsistency in user input:
> There were 4 GPU tasks found on node ubuntuserver16, but 3 GPUs were
> available. If the GPUs are equivalent, then it is usually best to have a
> number of tasks that is a multiple of the number of GPUs. You should
> reconsider your GPU task assignment, number of ranks, or your use of the
> -nb,
> -pme, and -npme options, perhaps after measuring the performance you can
> get.
>
> On Thu, Sep 13, 2018 at 4:11 PM Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > 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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