AMBER Archive (2007)

Subject: Re: AMBER: test submission through PBS queue

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Wed Jan 10 2007 - 13:33:09 CST

Hi,

On Wed, 10 Jan 2007, Evan Kelly wrote:

> I have just compiled the serial and parallel versions of Amber 9 on a
> cluster running PBS as a queuing system. I only have access to the
> parallel nodes through PBS, so I can't run the test suite (make
> test.parallel) as described in the installation instructions. Does
> anyone have a method in place to submit the test suite through a PBS
> script? Any suggestions would be greatly appreciated.

On this cluster mpiexec is a wrapper for mpirun that extracts the
machine details from pbs.

# AMBER Parallel Test Batch Script for mck
#
#PBS -N test2.2
#PBS -j oe
#PBS -m ae
#PBS -l walltime=0:20:00
#PBS -l nodes=2:ppn=2:myrinet
#PBS -S /bin/csh
set echo
setenv AMBERHOME /usr/local/amber/amber8
#
cd $AMBERHOME/test
setenv DO_PARALLEL mpiexec
make clean
make test.sander
make check
make clean
make test.sander.LES
make check
make clean
make test.pmemd
make check

Scott

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