MATLAB: Parallel computing on a cluster

clustermatlab 2014aParallel Computing Toolboxparforsubmat

I have a script test.m that includes parfor-loops.

In MATLAB 2014a on my personal computer it runs the parallel job perfectly.

On a huge Linux computer cluster it runs test.m perfectly if I have started MATLAB 2014a graphically through X on the frontend.

However, when submitting test.m to the queue it discards the parallelness and runs everything as in for-loops — on a single core on the given node.

What I write:

>> submat -q q12 test.m

q12 is the queue name.

Anyone with a clue??

Best Answer

My guess is that when you queue it, it launches MATLAB without Java. Java is required to use PCT. That also explains why it works fine when you X11 forward MATLAB. See below:

"The client session of MATLAB must be running the Java® Virtual Machine (JVM™) to use Parallel Computing Toolbox software."

http://www.mathworks.com/help/distcomp/programming-tips_f5-16100.html

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MATLAB: Is the communicating job stuck behind a concurrent job in queue in R2017b

The resolution is to avoid starting a parallel pool when submitting other jobs to the cluster.

The "parpool" object is generally used for interactive "parfor" or "smpd" operations. When the parallel pool is created with "parpool", it creates a concurrent job on the cluster that readies all of the workers to be available for when the user interactively calls "parfor" or "smpd". The concurrent job will continue running, causing other jobs to wait in queue until the parallel pool is shut down.

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This may indicate a syntax error in the script that is being submitted.

For example, in the test script below, the error message "qsub: directive error: V" is caused by a missing dash (-) before the "V" option:

#PBS -N my_job
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hostname

In the script above, the second to last line should be:

#PBS -V

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