Dear Terry,
Now i changed the path in the script file.
Openmpi is at /home/p_kumar/openmpi/bin/mpirun
using this I have recompiled amber12 in parallel. with export
DO_PARALLEL='mpirun -np 8' and using make test command amber12 installation
was successfully tested with no errors. But still after submitting the jobs
and while started running no output file was created.
any suggestions please
S.harikrishna
From: Terry <terrencesun.gmail.com<terrencesun.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20Problem%20in%20running%20parallel>>
Date: Wed, 31 Oct 2012 13:33:15 +0800
On Wed, Oct 31, 2012 at 12:56 PM, hari krishna <haricoolguy111.gmail.com>wrote:
*> Dear all, *
*> *
*> I have successfully installed serial and parallel version of AMBER12 in
the *
*> server (in my user user only) using gnu compiled openmpi. Also the test
was *
*> successfully completed. I used ./configure_openmpi in AmberTools/src for
*
*> openmpi. *
*> *
*> while using PBS script to run the program in parallel, in the queue, the
*
*> program is running and processors are allocated and the program is shown
*
*> like running in the server. But no output files are created in the given
*
*> folder even after long time. Please look at the following PBS script.
Any *
*> suggestions. *
*> *
*> *#!/bin/bash *
*> *
*> #PBS -l nodes=8:ppn=8 *
*> #PBS -l pmem=700mb *
*> #PBS -l walltime=600:00:00 *
*> *
*> export AMBERHOME=/home/p_kumar/amber12 *
*> export LD_LIBRARY_PATH=/home/p_kumar/amber12/lib:$LD_LIBRARY_PATH *
*> export DO_PARALLEL="$AMBERHOME/bin/mpirun -np 64" *
*> *
mpirun is not in $AMBERHOME.
Terry
*> *
*> cd /home/p_kumar/thioflavin/dynamics/parallel *
*> *
*> $DO_PARALLEL $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod.out -p *
*> complexsol.prmtop -c equil.rst -r prod.rst -x prod.mdcrd -ref equil.rst*
*
*> *
*> *
*> Sincerely *
*> S.Harikrishna *
*> _______________________________________________ *
*> AMBER mailing list *
*> AMBER.ambermd.org *
*>
http://lists.ambermd.org/mailman/listinfo/amber *
*> *
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