Dear Jiten,
Here is an example for running sander as a 4 processor job on 2 x dual cpu
machines using PBS and lam mpi. Note, if you use MPICH you will need to
modify this slightly. I hope this helps.
Ross
--------------------------------------
# Run sander job on 4cpu (2x2 redfish)
#PBS -l nodes=2:ppn=2
#PBS -l walltime=4:00:00
#PBS -l cput=16:00:00
#PBS -j oe
setenv LAMHOME /redfish/applications/case/mpi/lam/intel-8.0
setenv AMBERHOME /redfish/applications/case/amber8_lam_mpi/
setenv PATH /redfish/applications/case/mpi/lam/intel-8.0/bin:$PATH
#CHANGE THIS LINE TO POINT TO WHERE YOUR CALCULATION FILES ARE:
cd /redfish/people/userid/directory_for_calculation
setenv LAMRSH "rsh"
echo "NODES ALLOCATED = $PBS_NODEFILE"
cat $PBS_NODEFILE
lamboot -s $PBS_NODEFILE
lamnodes
#IF YOU CHANGE THE NUMBER OF CPUS REQUESTED DON'T FORGET TO CHANGE THE -np x
BELOW:
mpirun -np 4 $AMBERHOME/exe/sander -O -i ../mdin -o jac.out.4proc -c
.../inpcrd.equil -r restrt -p ../prmtop
lamhalt
echo "DONE"
--------------------------------------
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Jiten
Sent: 23 September 2004 08:45
To: amber.scripps.edu
Subject: AMBER: Amber job submission using PBS
Dear Amber users,
I am wondering if someone could provide me a template for the script for the
amber job submission using Portable Batch System (PBS).
Thanks in advance,
Sincerely,
N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Sep 23 2004 - 18:53:00 PDT
