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Matlab's Parallel Toolbox does not work well if you set a shell preference in your SGE request. If you otherwise use a #$ -S <shell> designation in your SGE qsub scripts, it is best to remove or comment them when submitting parallel Matlab jobs. |
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| This example demonstrates the -nojvm which disables some of Matlab's features in order to start faster and use less memory. This helps maintain the cluster's performance if you have a large batch of jobs which don't require the disabled features. |
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#!/bin/bash # The name of the job: #$ -N MatlabTest # Name of the output log file: #$ -o matjob.log # Combining output/error messages into one file: #$ -j y # Specifying the Queue #$ -q UI # One needs to tell the queue system to use the current directory as the working directory #$ -cwd # The command(s) to be executed: matlab -nodisplay -nodesktop -nojvm -r batch # Note after -r is the name of the routine or function |
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Submit the job using 'qsub parallel-test.sh', assuming the name of the submission script is called parallel-test.sh.
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Matlab's Parallel Toolbox requires Java, so if your code uses features of the toolbox, you must omit the -nojvm option when invoking matlab, otherwise your code will quit with an uninformative error. You can verify Java is available and otherwise deliberately quit with a helpful error message by adding this command before code which uses a feature requiring Java: error(javachk('jvm')) |
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#!/bin/bash # The name of the job: #$ -N test ## replace 'test' with job name # Name of the output log file: #$ -o matlabTest_parfor.log # Combining output/error messages into one file ( change y to n for separate files) #$ -j y # Specify the parallel environment (PE) and number of cores to use (8): #$ -pe smp 8 # One needs to tell the queue system to use the current directory as the working directory #$ -cwd # The matlab commands to be executed; replace "test" with your function name. # -r imediately runs a function without presenting an interactive prompt /opt/matlab/R2012b/bin/matlab -nodisplay -nodesktop -nosplash -r parafor-test |
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