MATLAB
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We don't have a license for MATLAB Distributed Compute Server (MDCS aka MDCE).
We do 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
/afs/ir.stanford.edu/software/matlab-2011b/bin/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.
$ 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 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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