[gmx-users] gromacs command in mpi single precision

[Peter Kroon]

Hi,

my personal solution to this is to tell mpirun to run 'gmx_mpi grompp'
just once on just one cpu: `mpirun -n1 -c1 gmx_mpi grompp ...`. But like
Mark wrote, it depends on your installed MPI whether this is needed.

Peter

On 29/06/16 10:49, Mark Abraham wrote:
> 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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