AMBER Archive (2007)

Subject: RE: AMBER: test submission through PBS queue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 10 2007 - 13:35:27 CST

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 -V

#PBS -M myemail_at_myaddress.edu

#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
Ross
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Evan Kelly
Sent: Wednesday, January 10, 2007 11:21
To: amber_at_scripps.edu
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
ebkelly_at_ualberta.ca

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