MATLAB

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(simple PCT run)
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== simple PCT run  ==
== simple PCT run  ==
-
<pre>/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop -r 'maxNumCompThreads'
+
<pre>matlab -nodesktop -r 'maxNumCompThreads'
&gt;&gt; matlabpool ( 'open', 'local', 8)
&gt;&gt; matlabpool ( 'open', 'local', 8)

Revision as of 21:05, 24 September 2012

Contents

first steps

Per FarmShare software try something like:

 module avail
 module load MATLAB-R2012a

If you're running MATLAB for the first time, it'll try to write some stuff into $HOME/.matlab so make sure you have your AFS tokens or else MATLAB will crash with an undecipherable error message.

PCT

We have the Parallel Computing Toolbox, you can use that to parallelize your job across multiple cores in a single machine.

Here's how to write a job using MDCS: http://docs.uabgrid.uab.edu/wiki/MatLab_CLI#Parallel_MATLAB

You can use the "maxNumCompThreads" command (deprecated) to see how many parallel threads you can run. I get "24" on barley, or "8" on corn.

simple PCT run

matlab -nodesktop -r 'maxNumCompThreads'

>> matlabpool ( 'open', 'local', 8)
Starting matlabpool using the 'local' configuration ... connected to 8 labs.
>> 
>> matlabpool size

ans =

     8

Then use 'parfor' instead of 'for'.

matlabpool of size 0 and size 1 are effectively the same, except the latter uses a PCT toolbox license.

Here are some training slides and example code that I copied from http://www.osc.edu/~samsi/sc11edu/

example single matlab file run via qsub

Here's our helloworld.m:

disp('Hello World');

Here's a command to run that.

 /afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop < helloworld.m

We want to run this same command via the job scheduling system. Let's write a job script.

#!/bin/bash

#$ -N matlab_example
#$ -m bes
#$ -M chekh@stanford.edu

/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop < /afs/ir/users/c/h/chekh/helloworld.m

Submit the script:

 qsub matlab_example.script

Look at the job status:

 qstat

You should get output file like matlab_example.oXXXXX

Warning: No display specified.  You will not be able to display graphics on the screen.
Warning: No window system found.  Java option 'MWT' ignored

                            < M A T L A B (R) >
                  Copyright 1984-2011 The MathWorks, Inc.
                    R2011b (7.13.0.564) 64-bit (glnxa64)
                              August 13, 2011

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
>> Hello World

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