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Revision as of 07:57, 16 July 2012 by Tanthony@uab.edu (Talk | contribs)

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Sample Job script for Amber

#!/bin/bash
#$ -S /bin/bash
#
# Example Amber job submission script can be found here:
#
# Execute from the current working directory
#$ -cwd
#
# Job runtime (1 hour, at 55 minutes Amber will be notified to shut down)
#$ -l h_rt=1:00:00,s_rt=0:55:00
#$ -j y
#
# Job Name and email
#$ -N ambertest_1
#$ -M YOUR_EMAIL_ADDRESS
# Email options to determine when to send emails
#$ -m be
#
#$ -pe openmpi 4
#
# Load the appropriate module(s)
. /etc/profile.d/modules.sh
 module load amber/amber-10-intel 
#
#$ -V
#$ -l vf=1G
#
mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI  -O -i file.in -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt