Bash / shell script for running Matlab jobs with the Sun Grid Engine. Qsub this whole script, rather than qsubbing Matlab directly.

matlab_np.sh

#!/bin/sh
# matlab_np.sh
#	Shell script to run a Matlab function from the bash shell
#		Ensure Matlab function is on the path first
#		NB Matlab breaks the bash shell, hence stty echo
#		stty echo works by itself; stty sane is just-in-case; haven't confirmed that it's necessary.
#		
#	Example usage: $ matlab_np.sh functionName 'string arg' arg2 ${arg3}...
#	Use with Qsub: $ ${QSUB_CMD} matlab_np.sh functionName arguments
#		NB do not Qsub matlab directly as your arguments won't be passed to the Matlab function
#	Nick Powell 2012-05-10

# # # # # # # # # # # # # # # # #
#      Passed-in Variables      #
# # # # # # # # # # # # # # # # #
# First argument is the function name in Matlab (ensure it's on the Matlab path)
functionName=$1
# The remaining arguments are arguments for the Matlab function
shift
arguments=$@

# # # # # # # # # # # # # # #
#      Fixed Variables      #
# # # # # # # # # # # # # # #
# Programs
MATLAB=/share/apps/matlabR2011b/bin/matlab

# # # # # # # # # # # # # # # # # # # # # # # #
#      Universal Variables and Functions      #
# # # # # # # # # # # # # # # # # # # # # # # #
source /home/npowell/scripts/universal_params_np.sh
source /home/npowell/scripts/functions.sh

# # # # # # # # #
#      Go!      #
# # # # # # # # #
time_start=`date +%s`
# Set up log file for the whole run
setUpLog ${BASH_SOURCE}
# Check directories
makeDirs ${logDir}
echoStatusTime "Running Matlab function: ${functionName} with arguments: ${arguments}"
# Do not qsub this directly; qsub this whole script instead.
${MATLAB} \
	-nodisplay \
	-r \
	"${functionName} ${arguments}; exit"
		
# ${MATLAB} -nodesktop -nosplash -nodisplay -r "${functionName} ${arguments}; quit;"
# Because Matlab breaks the shell on quitting otherwise:
stty echo
stty sane
time_end=`date +%s`
time_diff=$(( ${time_end} - ${time_start} ))
echo ""
echo "*******************************************************************************"
echoStatusTime "Matlab function ${functionName} complete! Took ${time_diff} seconds total."
echo "*******************************************************************************"
echo ""
completeFunc
# end