[gmx-users] regression test errors

[Dave M]

Hi Paul,

Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now.

Regarding tests, I found the folder here build/tests/regressiontests
So I checked all the log using a simple script (searching keyword
'Finished') and it shows that all the log files have Finished properly  in
their corresponding folders. So log files do not say anything here.

On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer <paul.bauer.q at gmail.com> wrote:

> Hello Dave,
>
> You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a MPI
> enabled build of GROMACS. This is what the error message tries to tell you,
> but we might need to improve on this.
>
> There should be a regressiontests folder somewhere in your build tree if it
> downloaded the tests correctly.
>
> Cheers
>
> Paul
>
> On Wed, 23 Oct 2019, 12:02 Dave M, <dave.gromax at gmail.com> wrote:
>
> > Hi Paul,
> >
> > Thanks for your reply.
> > a) I just checked there is no tests/regressiontests, some other folder is
> > there test/sphysicalvalidation
> > There is no log file.
> > b) Regarding thread-mpi I think it is not installed because when I use
> some
> > command like this:
> >
> >
> > gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2
> >
> > I get an error:
> >
> >
> > Fatal error:
> >
> > Setting the total number of threads is only supported with thread-MPI and
> > GROMACS was compiled without thread-MPI
> >
> > I think (please correct me) gmx_mpi is for external MPI  openMPI in my
> case
> > so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not
> > found. I am not sure what I missed in installation cmake flags.
> >
> > Dave
> >
> > On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer <paul.bauer.q at gmail.com>
> wrote:
> >
> > > Hello Dave,
> > >
> > > Did you have a look into the log files from the regression tests under
> > > tests/regressiontests?
> > > They might give us some insight into what is happening.
> > >
> > > The warning in respect to thread-MPI is harmless, it just tells you
> that
> > > you are using real MPI instead of thread-MPI.
> > >
> > > Cheers
> > > Paul
> > >
> > > On Wed, 23 Oct 2019, 07:36 Dave M, <dave.gromax at gmail.com> wrote:
> > >
> > > > Hi All,
> > > >
> > > > Any hints/help much appreciated why am getting regression tests
> > failure.
> > > > Also to mention I think thread-mpi was not installed as I got an
> error
> > > > saying "MPI is not compatible with thread-MPI. Disabling thread-MPI".
> > How
> > > > to check the compatibility?
> > > >
> > > > Thanks.
> > > >
> > > > best regards,
> > > > D
> > > >
> > > > On Sun, Oct 20, 2019 at 2:58 AM Dave M <dave.gromax at gmail.com>
> wrote:
> > > >
> > > > > Hi All,
> > > > >
> > > > > I am trying to install gromacs2019.4 with:
> > > > > cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
> > > > > -DGMX_MPI=on -DGMX_GPU=on
> > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
> > > > > -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug
> > > > >
> > > > > But 5 tests (41 to 46) were failed copied below:
> > > > >
> > > > >
> > > > > The following tests FAILED:
> > > > >
> > > > > 41 - regressiontests/simple (Failed)
> > > > >
> > > > > 42 - regressiontests/complex (Failed)
> > > > >
> > > > > 43 - regressiontests/kernel (Failed)
> > > > >
> > > > > 44 - regressiontests/freeenergy (Failed)
> > > > >
> > > > > 45 - regressiontests/rotation (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/Makefile2:1392: recipe for target
> > > > > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> > > > >
> > > > > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> > > > >
> > > > > CMakeFiles/Makefile2:1172: recipe for target
> > > 'CMakeFiles/check.dir/rule'
> > > > > failed
> > > > >
> > > > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > > > >
> > > > > Makefile:626: recipe for target 'check' failed
> > > > > make: *** [check] Error 2
> > > > >
> > > > > Not sure what could be wrong. Just to add I get some error/warning
> > > during
> > > > > installation which says "MPI is not compatible with thread-MPI.
> > > Disabling
> > > > > thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu
> > > 18.04
> > > > I
> > > > > used "sudo apt-get install openmpi-bin openmpi-common
> libopenmpi-dev"
> > > > >
> > > > > Please let me know how I can fix this.
> > > > >
> > > > > best regards,
> > > > > D
> > > > >
> > > > >
> > > > --
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