Submitting a Matlab Job to SGE
For more in-depth information, see the Matlab page.
To submit a single core Matlab job the following script may act as a template:
#!/bin/bash #$ -q long #$ -pe smp 1 # The MATLABPATH variable is set in the Matlab script to add additional # directories to the internal search paths. export MATLABPATH=directory_path_to_your_files.m:other_user_contrib_directory_path module load matlab matlab -nodisplay -nosplash -singleCompThread < your_file.m
Depending on your job, you might need to add -nojvm
Here are some notes on submitting Matlab jobs with PCT
#!/bin/bash #$ -q long #$ -pe smp 8 export MATLABPATH=path_to_matlab_file cd path_to_matlab_file module load matlab # The MATLABPATH variable is set in the Matlab script to add additional # directories to the internal search paths. matlab -nodisplay -nosplash < matlab_file
The Matlab file above includes the command
parpool('local',8), allowing Matalb to use 8 cores on the machine. Note that this number should match the number of cores requested from UGE.
Parallelization is done in a par for loop e.g.parpool('local',8); parfor i=1:N end
For further information, please consult the Matlab documentation: http://www.mathworks.com/support/