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How to run Matlab as batch mode jobs on clusters

Intro: The current examples and instructions listed in this page are mainly for the batch mode execution of matlab, and you donot need GUI interface or matlab distributing tool box to control your computation.

However, if you do need matlab GUI, you have two ways to do that

(a) If you are linux user, please allocate one computing node for xwindows, then start your matlab GUI from the computing node, please refer to "how to run interactive jobs" .

(b) If you are windows user, please use windows remote desktop to logon hpcwin.research.partners.org (you need to be inside PHS firewall), then start matlab GUI from there.

Note: if you need to load large image data in the GUI, we suggest you use (b) since hpcwin is networked with the cluster storage system.

For DCT/DCE related (distributed or parallel) jobs, please visit "How to distribute matlab jobs on HPRES cluster via Matlab DCE/DCT"

Step 1 to 4 only are needed if it is the first time for you to use matlab on HPRES cluster.

Step 1. Setup matlab environmnt.

a. Please read and finish "How to setup your working environment"

b Include the sentence of "module load matlab/default" in the module-loading blocks in your .bashrc file (you probably have it already)

c. Check your modules

 [testy@n137 ~] module list
 Currently Loaded Modulefiles:
  1) matlab/default

[testy@n137 ]$ echo $LD_LIBRARY_PATH
/source/matlab2007b/extern/lib/glnxa64

[testy@n137 ~]$ mkdir TestMatlab

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system
#BSUB -J myjob

# the following BSUB line specify the queue that you will use,
# please use bqueues command to check the available queues for each toolbox of matlab
# Bioinformatics toolbox, please use matlabbio queue
# Signal Processing toolbox, please use matlabsig queue
# Image Processing toolbox, please use matlabimg queue
# Wavelet toolbox, please use matlabwav queue
# Matlab DCE, please use matlabdce queue
# Matlab, Optimization and Statistic, please use matlab queue


#BSUB -q matlab


# the system output and error message output, %J will show as your jobID
#BSUB -o %J.out
#BSUB -e %J.err

#the CPU number that you will collect (Attention: each node has 2 CPU)
#BSUB -n 1


#when job finish that you will get email notification
#BSUB -u YourEmail@partners.org
#BSUB -N


#enter your working directory
cd /shr/home/$USER/TestMatlab


# Finally, Start the program
/source/matlab2007b/bin/matlab < myplot.m

[testy@n137 ~]$ bsub < testmat.lsf

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system, here it means you have 4 job elements
#BSUB -J matlabArray[1-4]

# the following BSUB line specify the queue that you will use,
# please use bqueues command to check the available queues for each toolbox of matlab
# Bioinformatics toolbox, please use matlabbio queue
# Signal Processing toolbox, please use matlabsig queue
# Image Processing toolbox, please use matlabimg queue
# Wavelet toolbox, please use matlabwav queue
# Matlab DCE, please use matlabdce queue
# Matlab, Optimization and Statistic, please use matlab queue

#BSUB -q matlab


# the system output and error message output, %J will show as your jobID
#BSUB -o "%J.%I.out"
#BSUB -e "%J.%I.err"

#the computing core number that you will collect for each job element
#BSUB -n 1


#when job finish that you will get email notification
#BSUB -u YourEmail@partners.org
#BSUB -N


#enter your working directory
cd /shr/home/$USER/TestMatlab


# Finally, Start the matlab and pass the paramter to the program, the parameter $LSB_JOBINDEX is system level
# variable from LSF queue. The value is from 1 to 4 (as indicated in job name) and will be distributed to each processor.
# You can associate this variable with your real parameters, your filenames ...etc
# To know more about job array, please check "how to submit massive jobs " webpage in this website.

/source/matlab2007b/bin/matlab -r 'manyplot($LSB_JOBINDEX)'

[testy@n137 TestMatlab]$ bsub < matlabarray.lsf