[gmx-users] regression test errors

[Paul Bauer]

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
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>