NOTE: The scripts on this page are very simple and are used ONLY as examples on how to submit jobs to the Biowulf cluster. Of course, users will typically submit much more compute-intensive jobs.

Sample file matlab.script

#!/bin/tcsh
#
#PBS -N Matlab
#PBS -m be 
#PBS -k oe
 
date

/usr/local/bin/matlab -nodesktop << EOF       #starts Matlab
a = 10;                                       #Matlab commands
b = 20;
c = 30;
d = sqrt((a + b + c)/pi);
exit
EOF                                            #end of Matlab commands

qsub -l nodes=1,matlab=1 /full/pathname/matlab.script

This qsub command requests one Matlab license ('matlab=1'), so the job will remain in the queue until a license is available. You will receive email when the job is executed and when it ends, because of the line PBS -m be in the script.

Create a swarm command file, named matlab_swarm_jobs for instance, with each line containing a single executable script.

Sample Matlab swarm command file:

/usr/local/bin/matlab -nodesktop < /data/user/run1.m
/usr/local/bin/matlab -nodesktop < /data/user/run2.m
/usr/local/bin/matlab -nodesktop < /data/user/run3.m
[...]

Submit this swarm command file matlab_swarm_jobs to the batch system with the command:

swarm -f matlab_swarm_jobs -l nodes=1,matlab=1
or
swarm -f matlab_swarm_jobs -l nodes=1,matlab=1,femlab=1,matlab-bio=1

depending on which Matlab licenses (resources) are required. More information about Matlab resources is in the next section.

Note that an unlimited number of jobs can be submitted to the queue, but the number that will actually run simultaneously depends on the per-user Matlab license limit, and the number of available licenses. The batch system will restrict the number of Matlab licenses that are allocated to an individual user. This limit is subject to change depending on the number of licenses and usage.

qsub -l nodes=1:m2048,matlab=1 my_job_script

Similarly, a job that requires the Bioinformatics toolbox should be submitted as:

qsub -l nodes=1,matlab=1,matlab-bio=1 my_job_script

If using Matlab interactively, the same resources must be specified:
(user input in bold)

biowulf% qsub -I -l nodes=1,matlab=1
qsub: waiting for job 801552.biobos to start
qsub: job 801552.biobos ready

p574% matlab
                                       < M A T L A B >
                           Copyright 1984-2004 The MathWorks, Inc.
                                  Version 7.0.0.19901 (R14)
                                         May 06, 2004
>> ....
>> exit

p574% exit
logout

qsub: job 801552.biobos completed

biowulf%

The available toolboxes and corresponding resource names are listed in the following table:

A '-' indicates that the toolbox is not licensed, and therefore no resource needs to be specified. Note that an unlimited number of jobs can be submitted to the queue, but they will run depending on the number of available licenses and the per-user license limit.

To run the MATLAB graphics interface, an X windows connection to Biowulf is required. Open an Xwindows connection to biowulf.nih.gov, and check that it is working by typing 'xclock' at the Biowulf prompt. Now allocate an interactive node with the '-V' flag to transfer all your environment variables to the computational node. Example:

     biowulf% qsub -I -l nodes=1,matlab=1 -V
     qsub: waiting for job 423061.biobos to start
     qsub: job 423061.biobos ready

     [username@p955 ~]$ matlab&

You must use Xwindows software to connect to Biowulf if you want to use the Matlab GUI. For batch jobs, or for non-GUI interactive jobs, Xwindows is not required. <>

It is also possible to run Matlab interactively on the command-line, without the GUI. This would typically be useful only for debugging. Again, this should be done by allocating an interactive node. Example:

     biowulf% qsub -I -l nodes=1,matlab=1,matlab-spline=1
     qsub: waiting for job 2011.biobos to start
     qsub: job 2011.biobos ready

     p139$ matlab
      
                          < M A T L A B (R) >
                  Copyright 1984-2008 The MathWorks, Inc.
                       Version 7.7.0.471 (R2008b)
                           September 17, 2008


  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
           
     >> quit
     [username@p139 ~]$ exit
     logout

     qsub: job 2011.biobos completed
     biowulf $ 

Versions

-------------------------------------------------------------------------------------
MATLAB Version 7.7.0.471 (R2008b)
MATLAB License Number: 35
Operating System: Linux 2.6.18-92.el5 #1 SMP Tue Jun 10 18:51:06 EDT 2008 x86_64
Java VM Version: Java 1.6.0_04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit 
Server VM mixed mode
-------------------------------------------------------------------------------------
MATLAB                                                Version 7.7        (R2008b)
Simulink                                              Version 7.2        (R2008b)
Bioinformatics Toolbox                                Version 3.2        (R2008b)
Curve Fitting Toolbox                                 Version 1.2.2      (R2008b)
Image Processing Toolbox                              Version 6.2        (R2008b)
Neural Network Toolbox                                Version 6.0.1      (R2008b)
Optimization Toolbox                                  Version 4.1        (R2008b)
Partial Differential Equation Toolbox                 Version 1.0.13     (R2008b)
Signal Processing Toolbox                             Version 6.10       (R2008b)
SimBiology                                            Version 2.4        (R2008b)
Spline Toolbox                                        Version 3.3.5      (R2008b)
Statistics Toolbox                                    Version 7.0        (R2008b)
Symbolic Math Toolbox                                 Version 5.1        (R2008b)
System Identification Toolbox                         Version 7.2.1      (R2008b)
Wavelet Toolbox                                       Version 4.3        (R2008b)