Here are three simple scripts to submit and run MATLAB scripts on a cluster via Sun's Grid Engine (SGE). We run this on our ROCKS Cluster, but it should work anywhere that SGE is used.

• submit_jobs.sh
  • Run this script from the command line.
  • It submits an array job to the SGE cluster queue which runs multiple copies of the jobs.sh script.
  • You need to modify this to change the number of jobs you want. (i.e., jobs 1:65 will produce 64 jobs numbered 1 to 64.)
• job.sh
  • This script is run on the cluster nodes by the cluster queue.
  • It runs MATLAB with the correct command line arguments to run it silently.
  • It tells MATLAB to run the matlab_job.m file.
  • You need to modify this to change the path to matlab and the path to your stderr and stdout files.
• matlab_job.m
  • This file tries to get the Task ID (SGE_TASK_ID) of the job.
  • If it doesn't find a Task ID it sets it to -1.
  • If the Task ID is not -1, this script exits MATLAB at the end. (If you don't do this it will never quit.)
  • You need to modify this file so that it starts the appropriate computation based on the job ID.

All scripts are Copyright 2007 by David Black-Schaffer. Permission to use and/or modify them is freely given. I am not responsible for any errors or problems associated with them!