RE: AMBER: test submission through PBS queue

From: Ross Walker <>
Date: Wed, 10 Jan 2007 11:35:27 -0800

Dear Evan,
You should be able to run the make test.parallel through PBS.
Here is an example PBS script that I use on SDSC's teragrid cluster:
#SDSC Teragrid PBS Script

#PBS -j oe

#PBS -l nodes=2:ppn=2

#PBS -l walltime=0:30:00

#PBS -q dque



#PBS -A accountcode

#PBS -N run_sander_4_test

cd /gpfs/mydir/amber_job
export DO_PARALLEL="mpirun -v -machinefile $PBS_NODEFILE -np 4 "
export AMBERHOME=/usr/local/apps/amber9/
cd $AMBERHOME/test
make test.parallel

All the best

|\oss Walker

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| San Diego Supercomputer Center |
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From: [] On Behalf Of
Evan Kelly
Sent: Wednesday, January 10, 2007 11:21
Subject: AMBER: test submission through PBS queue

Hi Everyone,

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.

Thanks in advance!

Evan Kelly

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Received on Sun Jan 14 2007 - 06:07:14 PST
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