[gmx-users] gromacs command in mpi single precision

[Mark Abraham]

Hi,

The MPI build only installs gmx_mpi, so that's the prefix you need for the
other tools. But there is no purpose in so doing because the tools don't
use such parallelism (and mpirun -np 64 gmx_mpi grompp will try to write 64
of the same .tpr file...). Some MPI will permit you to just run "gmx_mpi
grompp" without mpirun, which is convenient.

Mark

On Wed, Jun 29, 2016 at 8:24 AM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Dear gromacs user,
>
> What are the gromacs command on parallel mdrun in single precision in 5.1.2
> version?
> I just know the "gmx mdrun" changes to "mpirun gmx_mpi mdrun" as you can
> see in below script, but how about otheres? for example "gmx grompp" ?
>
>
> #$ -A gromacs_parallel
> #$ -pe orte_sl16* 32
> . /etc/profile.d/modules.sh
> module load openmpi-1.6.3/icc/1.6.3
> module load intel/intelPSXE2011SP1-64
>
> mpirun gmx_mpi mdrun -ntomp 1 -deffnm eql1 -s eql1.tpr >C.log 2>&1
> joberror=$?
> exit $joberror
>
> Thanks,
> Regards,
> Alex
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