- Original Message -
From: #ZHAO LINA# zhao0...@ntu.edu.sg
Date: Friday, January 29, 2010 1:11
Subject: [gmx-users] mpi_run issue
To: gmx-users@gromacs.org
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.
We can't know the best procedure for your cluster because we haven't read its
documentation or talked to its admins... (hint, hint)
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
This looks wrong. PBS usually has flags that let you specify running the job in
directory from which submission occured - use them.
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
If PBS is defining $PBS_NODEFILE to point to some file it creates, then that
file won't be local to the directory you've arbitrarily changed to, so NCPUS
won't get defined suitably, so mpirun won't work.
I'd suggest you start again from some example script that is known to work on
your cluster and modify only the mpirun line.
Mark
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
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