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Sample Job script for Amber

Next, create a job submit script as shown below called 'amberSubmit', make sure to edit the following parameters:

 * s_rt to an appropriate soft wall time limit
 * h_rt to the maximum wall time for your job
 * -N - job name
 * -M - user email
 * -pe openmpi numberOfProcessors  (-pe openmpi 8 - run the code in parallel on 8  processors on the Cheaha compute nodes.)
 * -l vf to the maximum memory needed for each task
 * cd to the current working directory where the job data is stored
 * Replace file.{in,out,restrt,prmtop,cmd} name with your files. 
#$ -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
# Email options to determine when to send emails
#$ -m be
#$ -pe openmpi 4
# Load the appropriate module(s)
. /etc/profile.d/
 module load amber/amber-10-intel 
#$ -V
#$ -l vf=1G
mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI  -O -i -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt

Submit the script to the scheduler with

$ qsub amberSubmit

The output will be

Your job 82341234 ("ambertest_1") has been submitted