[gmx-users] Testing mpi version of Gromacs 5.1

[Szilárd Páll]

On Thu, Oct 8, 2015 at 11:56 AM, Joachim Hein <joachim.hein at math.lu.se>
wrote:

> Hi everyone
>
> I hope this is the right place to discuss this.
>
> I am having issues with checking the correctness of my mpi version of
> Gromacs 5.1.  I have build and tested earlier versions without issues (e.g.
> 5.0.4 is the latest I did).  I am also building float and double versions
> of the serial tools and they test without issue using: make check.
>
> I tried two things to test my MPI build (I’ll give a detailed account on
> how I build later):
>
>  make -j 8 check
>
> on a back-end node (slurm sbatch job asking for 8 cores) of our cluster.
> Tests 19 to 25 pass, while the first 18 fail in MPI_Init.  Is that how it
> is supposed to be?
>
> The other test I tried was as follows:
>
> - change into the regression test directory
> - source the GMXRC file of an install containing a float and a float mpi
> version
> - executing: ./gmxtest.pl all -np 4  (in a batch script asking for 4
> cores)
>
> I get the following:
>
>  gmx-completion.bash: line 258: `_gmx_convert-tpr_compl': not a valid
> identifier
>

This error clearly suggests that something is wrong with the bash
completion script when used with your bash version. This sounds like an
issue that likely requires some dev attention, so please file an issue at
redmine.gromacs.org (and include the info you provided + your bash version).

As a workaround, you could disable bash completion e.g. by removing
the $GMXBIN/gmx-completion.bash file or disabling loading it in
$GMXBIN/GMXRC.bash:75.

Cheers,
--
Szilárd


>
>
> So here comes the detail on the build:
> -----------------------------------------------------------
>
> gcc/5.2.0
> openmpi 1.10.0 build for the above gcc 5.2.0
> fftw 3.3.4 build for the above gcc with sse and avx
> boost/1.59.0
>
> CMAKEFLAGS="-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DGMX_FFT_LIBRARY=fftw3 -DBUILD_SHARED_LIBS=ON
> -DCMAKE_INSTALL_PREFIX=$PREFIX -DGMX_DEFAULT_SUFFIX=ON -DREGRESSION
> TEST_PATH=$RTESTPATH -DGMX_SIMD=AVX_128_FMA
> -DCMAKE_PREFIX_PATH=$FFTW3_HOME"
>
> I build the serial and parallel version:
>
> # Building single precision without MPI
> BUILDDIR="bdir_float_boost"
> mkdir -p $BUILDDIR
> cd $BUILDDIR
>
> cmake ../ $CMAKEFLAGS
>
> make -j 16
>
> make -j 4 check
>
> make install
>
> cd ..
>
> # Building single precision with MPI
> BUILDDIR="bdir_float_mpi_boost"
> mkdir -p $BUILDDIR
> cd $BUILDDIR
>
> cmake ../ $CMAKEFLAGS -DGMX_MPI=ON -DBUILD_SHARED_LIBS=off
>
> make -j 16
>
> make install
>
>
> Both installs go to the same directory.  This procedure is essentially the
> same as I used fro Gromacs 5.0.4.
>
> I tested with gcc 4.9.0 and openmpi 1.8.3 (which I used for gromacs 5.0.4)
> and the results are similar, though the error message from the MPI_Init is
> slightly different.
>
> Any comments and help is greatly appreciated.
>
> Thanks and best wishes
>   Joachim
> --
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