Dear All,
I am submitting my sander.MPI job with qsub using the following script
#!/bin/sh
#$ -S /bin/bash
# This is file Run__amber
#PBS -l nodes=4:ppn=4
#PBS -V
#PBS -N Imtiaz
#PBS -l walltime=03:59:00
cd $PBS_O_WORKDIR
echo "simulation started at" `date`
/opt/lam/7.1.3/bin/lamboot
/opt/amber10/bin/sander.MPI -O -i heat.in -o heat.out -p SAMP.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst
echo "simulation end at" `date`
When I submit the job with qsub I get a job ID and showq indicate that job is running on 16 processors and 4 nodes.
414013 mis9 Running 16 03:55:33 Sat Jan 30 00:58:54
1 Active Job 16 of 36 Processors Active (44.44%)
4 of 9 Nodes Active (44.44%)
When I noticed the this job is taking very long time then an average estimate I used ssh to each note and run top command. I found sander.MPI is running only on one node.
What could be the potential reasons that despite job is submitted to 4 nodes and showq also show that it is running on four nodes but in reality it is taking unnecessarily very long time and top command on each individual nodes shows that sander.MPI is actually running only on one node ? Do I need to change or submit some environmental variables in the job submission script
Waiting for some suggestion in this regards.
Imtiaz
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Received on Sat Jan 30 2010 - 07:30:03 PST
