[gmx-users] regression test errors

[Dave M]

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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