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-	We have a trial version of MATLAB Distributed Compute Server until 2011-12-25.	+	==example single matlab file run via qsub==
-	The standard MATLAB install in AFS now also has R2011b in addition to R2010b.	+	Here's our helloworld.m:
		+	<pre>
		+	disp('Hello World');
		+	</pre>
-	You will need to write your MATLAB code to use the Parallel Computing Toolbox before using the Distributed Computing Server.	+	Here's a command to run that.
		+	/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop < helloworld.m
-	Here's how to write a job using MDCS: http://docs.uabgrid.uab.edu/wiki/MatLab_CLI#Parallel_MATLAB	+	We want to run this same command via the job scheduling system. Let's write a job script.
-	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==
	<pre>		<pre>
-	/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop -r 'maxNumCompThreads'	+	$ cat matlab_example.script
		+	#!/bin/bash
-	>> matlabpool ( 'open', 'local', 8)	+	#$ -N matlab_example
-	Starting matlabpool using the 'local' configuration ... connected to 8 labs.	+	#$ -m bes
-	>>	+	#$ -M chekh@stanford.edu
-	>> matlabpool size	+
-	ans =	+	/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop < /afs/ir/users/c/h/chekh/helloworld.m
-		+
-	8	+
-		+
-	Then use 'parfor' instead of 'for'.	+
	</pre>		</pre>
-	matlabpool of size 0 and size 1 are effectively the same, except the latter uses a PCT toolbox license.	+	Submit the script:
		+	qsub matlab_example.script
-	Here are some training slides and example code that I copied from http://www.osc.edu/~samsi/sc11edu/	+	Look at the job status:
-	* http://stanford.edu/~chekh/matlab.tar	+	qstat
-	==example single matlab file run==	+	You should get output files like matlab_example.script.eXXXXX and matlab_example.script.oXXXXX
-		+
-	Here's our helloworld.m:	+
-	<pre>	+
-	disp('Hello World');	+
-	</pre>	+
-		+
-	Here's a command to run that.	+
-	/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop < helloworld.m	+

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Revision as of 13:36, 18 January 2012

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.

$ cat matlab_example.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 files like matlab_example.script.eXXXXX and matlab_example.script.oXXXXX