The following script is useful for starting Matlab scripts on remote machines using SSH. It solves the following issues:

• Matlab interpreting '&' as input file
• Start script without file ending
• Loosing matlabs output
• Typing in the full command

Matlab script starter

#!/usr/bin/env bash
#
# This script starts a Matlab session in the background using the
# *.m - script given as first argument.
#
# Matlabs output is written to the file 'log.txt'.
#
# For handy usage (Just call 'mls <script>') add this line to your
# bash_alias:
#     alias mls="sh ~/.matlab/mlScriptStarter.sh"
#
 
# Check, if argument is given
if [ -z "$1" ]; then
    echo "At least one argument required. Syntax: ./startMatlab.sh INFILE"
    return 1
else
    INFILE="$1"
fi
 
# Remove the file ending
if [ "${INFILE##*.}" = "m" ]; then
    BASE="${INFILE%%.*}"
else
    BASE="$INFILE"
fi
 
# Start Matlab
# ------------
# Some matlab options (see 'matlab -help' for more):
#     -nojvm        Shut off all Java support by not starting the
#                   Java virtual machine. In particular the MATLAB
#                   desktop will not be started.
#
#     -nodesktop    Do not start the MATLAB desktop. Use the current
#                   terminal for commands. The Java virtual machine
#                   will be started.
#
#     -nodisplay    Do not display any X commands. The MATLAB
#                   desktop will not be started. However, unless
#                   -nojvm is also provided the Java virtual machine
#                   will be started.
#
#     -nosplash     Do not display the splash screen during startup.
#
# Bash commands:
#     >    Pipe output to file
#     &    Background job
 
matlab -nodisplay -nosplash -r "${BASE}" > log.txt &
 
return 0

Save the code for example to ~/.matlab/mlScriptStarter.sh and make it executable.

Compile your m.script and all m-scripts with functions you have included. Your StandaloneScript.m should not depend on parameters (can but complicated).

 mcc -mv -o NameOfExecutable StandaloneScript.m FunctionScript1.m Functionscript2.m ...

For running the Executable you have to show the way to the matlab runtime libraries:

export LD_LIBRARY_PATH=/usr/local/matlab/research/runtime/glnxa64:/usr/local/matlab/research/bin/glnxa64:/usr/local/matlab/research/sys/os/glnxa64

or respectively for the woody cluster:

export LD_LIBRARY_PATH=/apps/matlab/R2014a/runtime/glnxa64:/apps/matlab/R2014a/bin/glnxa64:/apps/matlab/R2014a/sys/os/glnxa64

Then you can call the Executalbe itself:

./NameOfExecutable [parameters]

The mcc compiler also creates a shell script run_NameOfExecutable.sh which you can use to run your new binary file. As Parameter it needs the path to the matlab environment.

./run_NameOfExecutable.sh /usr/local/matlab/research

http://scv.bu.edu/examples/matlab/misc/standaloneDemo/standaloneDemo.zip

Includes description on how to run the compiled standalone programms on cluster with qsub http://www.bu.edu/tech/support/research/software-and-programming/common-languages/matlab/standalone/