[gmx-users] mpi_run issue

[#ZHAO LINA#]

Hi,

I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place wrong, seems no files came out after several hours running
Is anyone please help me to modify it, and how can know the process of its running in the cluster.

Thanks and best regards,

Elsa

#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne

## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V

## To run on 16 cpus
#PBS -l nodes=2:ppn=8

PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1

cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em 
exit 0

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