I have access to a 128-core cluster on which I would like to run a parallelised job. The cluster uses Sun GridEngine and my program is written to run using Parallel Python, numpy, scipy on Python 2.5.8. Running the job on a single node (4-cores) yields an ~3.5x improvement over a single core. I would now like to take this to the next level and split the job across ~4 nodes. My qsub
script looks something like this:
#!/bin/bash
# The name of the job, can be whatever makes sense to you
#$ -N jobname
# The job should be placed into the queue 'all.q'.
#$ -q all.q
# Redirect output stream to this file.
#$ -o jobname_output.dat
# Redirect error stream to this file.
#$ -e jobname_error.dat
# The batchsystem should use the current directory as working directory.
# Both files will be placed in the current
# directory. The batchsystem assumes to find the executable in this directory.
#$ -cwd
# request Bourne shell as shell for job.
#$ -S /bin/sh
# print date and time
date
# spython is the server's version of Python 2.5. Using python instead of spython causes the program to run in python 2.3
spython programname.py
# print date and time again
date
Does anyone have any idea of how to do this?