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Parallel Matlab

Systems & Access :: Learning to Use :: Linux Computing Resource

MathWork's MATLAB R2009a computational software, with the Distributed Computing Engine and Parallel Computing Toolbox is now available on the HPCC Linux Cluster.

You can access the software by using the standard shared software method below:

for (t)csh shell:
if (-e /usr/usc/matlab/2009a/setup.csh) then
	source /usr/usc/matlab/2009a/setup.csh
endif
for bash shell:
	source /usr/usc/matlab/2009a/setup.sh

After running the appropriate command from above, please follow the steps below.

  1. Follow the steps that you usually take to launch the MATLAB program
  2. Once the program interface diplays, select Manage Configurations from the Parallel menu near the top left of the screen. A Configurations Manager window will open
  3. From the File menu, select New and then Torque to create an appropriate torque-based configuration for the Linux Cluster.
Important Configuration Options
  • "Root directory of MATLAB installation for workers"
    should be set to "/usr/usc/matlab/2009a/".
  • "Number of workers available to scheduler"
    should be set to the number of processors your job will run on.
  • "Directory where job data is stored"
    should be where you want to write your output files to.
  • "Job data location is accessible from both client and cluster nodes"
    should be set to "True".
  • "Remote shell command to call on UNIX when running parallel jobs (RshCommand)"
    should be "ssh".

Additional Options

You may wish to experiment with other options in order to accomplish your specific goals. If you need to submit jobs to a specific queue, you can use the option:
"Additional command line arguments for job submission (SubmitArguments)" with a value like "-q specificqueuename".

You can also use this setting to request specific node types ie: "-l arch=x86_64".

In order for you parallel jobs to run correctly, you will need to add the appropriate 'source /usr/usc/matlab/2009a/setup.*' command into your .cshrc ((t)csh shell) or .bashrc (bash shell) so that jobs you submit through MATLAB will have access to the correct version of MATLAB. If you are logged into hpc-login2 and running MATLAB there, you should no use the qsub command.

For (t)csh:
if (-e /usr/usc/matlab/2009a/setup.csh) then
	source /usr/usc/matlab/2009a/setup.csh
endif

For bash:

if [ -e "/usr/usc/matlab/2009a/setup.sh" ]; then
	/usr/usc/matlab/2009a/setup.sh
fi

More detailed MATLAB documentation, please visit the Mathworks help website.

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