Hi Imtiaz
From what you describe it looks like sander is doing exactly what you
asked it to, run on one node.
I see no mpirun or mpiexec in front of the executable argument. Check
the docs for your cluster for the exact argument but it should look
something like:
mpirun -np 16 --machinefile $PBS_NODEFILE $AMBERHOME/exe/sander.MPI
This runs 16 mpi threads which should, if your queing system built the
machine file right, run over 4 nodes, 4 on each node.
Good luck
Ross
On Jan 30, 2010, at 7:20, MUHAMMAD IMTIA SHAFIQ
<imtiazshafiq.gmail.com> wrote:
> Dear All,
>
> I am submitting my sander.MPI job with qsub using the following script
>
> #!/bin/sh
> #$ -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 - 10:00:03 PST
