Re: FW: Parallel Simulations

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Feb 06 2010 - 10:40:15 CST

On Sat, Feb 6, 2010 at 10:56 AM, #SHEPHERDSON IGNATIUS MARK#
<SHEP0001_at_ntu.edu.sg> wrote:

> Hi,
>
> I am trying to run parallel simulations on cluster computers. However, when
> i specify 2 processors to use, I get 2 different processors running serially
> twice on my log file, giving me 2 results instead of 1. Is there something
> wrong with my script file?

the script is very dependent on your local installation.
it is more likely, however, that your namd binary is not
correctly compiled.

axel.

>
> #!/bin/sh
>
> #$ -V
>
> #$ -cwd
>
> #$ -N NAMD
>
> #$ -pe mpich-eth 2
>
> #/usr/voltaire/mpi/bin/mpirun_ssh -np $NSLOTS -hostfile $TMPDIR/machines
> ./integral
>
> export
>
> ls -l $TMPDIR/machines
>
> cat $TMPDIR/machines
>
> MPIRUN=/usr/local/openmpi/intel/bin/mpirun
>
> ls -l $MPIRUN
>
> $MPIRUN -np 2 -machinefile $TMPDIR/machines
> /home/students/FYP_Lim2/Ignatius/NAMD_2.7b1_Source/Linux-x86_64 g++/namd2
> /home/students/FYP_Lim2/Ignatius/NAMD_2.7b1_Source/test1/z.conf>z.log
>
>
>
> Thank you.
>
> Ignatius
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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