HPCC

Center for High-Performance Computing and Communications

Parallel MATLAB

MathWorks’ MATLAB computational software with the Distributed Computing Engine and Parallel Computing Toolbox is currently installed on the HPCC Linux cluster.

To access the software, source the files listed below.

For (t)csh Shell

if (-e /usr/usc/matlab/default/setup.csh) then
source /usr/usc/matlab/default/setup.csh
endif

For bash Shell

if [ -e /usr/usc/matlab/default/setup.sh ]; then
source /usr/usc/matlab/default/setup.sh
fi

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

  1. Launch MATLAB.
  2. Once the program interface displays, select Manage Configurations from the Parallel menu near the top left-hand side 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/default/.
  • 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 the directory to which you want to write your output files.
  • 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 set to 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 such as  -q
specificqueuename
.

You can also use this setting to request specific node types, i.e: -l arch=x86_64.

In order to run parallel jobs to run correctly, you will need to add the appropriate command into your .cshrc, if you are using the (t)csh shell, or .bashrc, if you are using the bash shell) so that jobs you submit through MATLAB will have access to the correct version of MATLAB.

If you are running MATLAB on hpc-login2, you should not use the qsub command. MATLAB will generate job submission scripts that will issue the qsub command for you, depending on how you utilize the Parallel Toolbox.

Getting Help

For additional information on MATLAB, please visit the Mathworks help website. For any questions related specifically to using Parallel MATLAB on HPCC, send an email to hpcc@usc.edu.