ARCHIVED: Use MATLAB on Big Red II at IU

• Overview
• Set up your user environment
• Submit a MATLAB batch job
• Run MATLAB interactively
• Get help

Overview

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.

Set up your user 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, see Use modules to manage your software environment on IU research supercomputers.

Submit 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 (for example, matlab_input.m) containing the commands MATLAB should run.
2. Create a job script (for example, 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 

Run MATLAB interactively

  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 (for example, 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

Get help

If you need help or have a question about using MATLAB on Big Red II, contact the UITS Research Applications and Deep Learning team.