At IU, on Big Red II, how do I use MATLAB?

On Big Red II at Indiana University, you can use MATLAB interactively from the command line or in batch mode using a TORQUE job script. If your interactive session will require more than 20 minutes of processor time, you must run it as an interactive job on one of Big Red II's compute nodes in the Cluster Compatibility Mode ( CCM) execution environment.

On this page:


Setting up your user environment

On the research computing resources at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.

To use MATLAB on Big Red II, you must first add the matlab module to your user environment. To run MATLAB jobs on Big Red II's compute nodes in the CCM execution environment, you also must add the ccm module to your user environment. To make sure both modules are loaded every time you log into Big Red II, add the following lines to your ~/.modules file:

  module load matlab 
  module load ccm

For more about using Modules to configure your user environment, see On the research computing systems at IU, how do I use Modules to manage my software environment?

Submitting a MATLAB batch job

To submit a MATLAB batch job that will run on Big Red II's compute nodes in the CCM execution environment:

  1. Create an m-file (e.g., matlab_input.m) containing the commands MATLAB should run.
  2. Create a job script (e.g., matlab_job) for the TORQUE resource manager on Big Red II. Your job script must include the ccmrun command, which will launch MATLAB on a compute node in the CCM environment, and the -l gres=ccm flag.

    For example (replace username with your IU username and username@iu.edu with your IU email address):

     #!/bin/bash 
     #PBS -l nodes=1:ppn=32
     #PBS -l walltime=00:10:00
     #PBS -l gres=ccm
     #PBS -m ae
     #PBS -M username@iu.edu
     #PBS -N matlab_job_name
     #PBS -V
     
     cd /N/u/username/BigRed2/new_directory
    
     ccmrun matlab -r matlab_input

    The above example job script will:

    • Change the working directory to the directory where the matlab_input.m m-file is located.
    • Invoke ccmrun to launch MATLAB.
    • Have MATLAB run the commands in the m-file (with the -r option, you can leave off the m-file's .m extension).
    • Have Big Red II email you when the job is complete.
  3. Submit the job script to the TORQUE resource manager; on the command prompt, enter:
      qsub matlab_job
  4. To check the status of your job, use the qstat command (replace username with your IU username):
      qstat -u username 

Running MATLAB interactively

Note:

If your interactive session will require less than 20 minutes of processor time, you can load the matlab module and launch the application from the Big Red II command line; for example:

  jajbinks@login1:~> module load matlab
  jajbinks@login1:~> matlab

Interactive sessions requiring more than 20 minutes of processor time must be run as interactive jobs on a Big Red II compute nodes in the CCM execution environment. This method of interactive execution is strongly recommended, as the login nodes are not intended for computational work.

To run an interactive MATLAB job on Big Red II:

  1. Make sure your user environment is configured properly; see Setting up your user environment above.
  2. From the command line, enter the qsub command with the -I (interactive), -l gres=ccm, and -q cpu (CPU queue) flags added; for example:
      jajbinks@login1:~> qsub -I -l walltime=01:00:00 -l nodes=1:ppn=32 -l gres=ccm -q cpu  

    When the resources needed to run your job are available, your job will start. Once the CCM execution environment is initialized, you'll be placed on one of Big Red II's aprun nodes:

      qsub: waiting for job 79064 to start
      qsub: job 79064 ready
      
      In CCM JOB:  79064  JID  79064  USER  jajbinks  GROUP  uits
      Initializing CCM environment, Please Wait
      waiting for jid....
      CCM Start success, 1 of 1 responses
      Directory: /N/u/jajbinks/BigRed2
      Tue Sep 10 15:29:21 EDT 2013
      jajbinks@aprun1:~>
  3. From the aprun command line, enter the ccmlogin command:
      jajbinks@aprun1:~> ccmlogin

    This will place you on a Big Red II compute node (e.g., nid00885):

      Warning: Permanently added '[nid00885]:203' (RSA) to the list of known hosts.
      jajbinks@nid00885:~>
  4. From the compute node command prompt, enter matlab to launch MATLAB:
      jajbinks@nid00885:~> matlab
      Warning: No display specified.  You will not be able to display graphics on the screen.
      Warning: No window system found.  Java option 'Desktop' ignored.
      
                                  < M A T L A B (R) >
                        Copyright 1984-2013 The MathWorks, Inc.
                          R2013a (8.1.0.604) 64-bit (glnxa64)
                                   February 15, 2013
      
      No window system found.  Java option 'Desktop' ignored.
      
      To get started, type one of these: helpwin, helpdesk, or demo.
      For product information, visit www.mathworks.com.
      
      >>

To use the features of the MATLAB graphical user interface (GUI), you must SSH to Big Red II with X forwarding enabled, and then use qsub with the -I (interactive) and -X (X forwarding) switches, as well as the -l gres=ccm switch; for example:

  jajbinks@login1:~> qsub -I -X -l walltime=00:02:00 -l nodes=1:ppn=32 -l gres=ccm -q cpu

For instructions on setting up and using X forwarding, see On my personal computer, how do I use X forwarding to securely run graphical applications installed on IU's research computing systems?

Getting help

Support for IU research computing systems, software, and services is provided by various UITS Research Technologies units. For help, see Research computing support at IU.

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This is document bdns in the Knowledge Base.
Last modified on 2017-11-15 09:19:50.

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