Bash script error to run MATLAB

Question

I'm trying to run a matlab script (ga_opt_main.m) in a cluster. I have to write a job submission file, which is essentially just a shell script. But I have never written a shell script and this is what I wrote

  #!/bin/bash
  #PBS -q *queuename*
  #PBS -l nodes=1:ppn=20
  #PBS -l walltime=02:00:00
  #PBS -N ga_opt_main

  module load matlab/R2011b
  module list

  unset DISPLAY
  matlab -nodisplay -nodesktop -r *directory path/ga_opt_main.m*

MATLAB opens in the background but my job is not run. Instead I get an error file saying

  bash: -c: line 0: syntax error in conditional expression
  bash: -c: line 0: syntax error near `fraction'

Any ideas on why this occurs and how it can be avoided? Thanks!

I've never used PBS before, but it looks like the words in between the asterisks are placeholder text that you are supposed to replace with something else. For example #PBS -q *queuename* looks a little fishy.... — Cypress Frankenfeld
– Cypress Frankenfeld, Commented Aug 4, 2012 at 0:29
@CypressFrankenfeld: anything passed in between -r "..." must be correct commands as you would type them in MATLAB command window in the IDE. To run a script, you either browse to the same directory as the file or you add its folder to the path, then call it by name (or use the RUN function as I've showed). — Amro
– Amro, Commented Aug 4, 2012 at 0:36
@Amro, you are completely correct. I'll delete that post and just refer to your answer. — Cypress Frankenfeld
– Cypress Frankenfeld, Commented Aug 4, 2012 at 0:46
You may need to replace *directory path/ga_opt_main.m* with a Matlab command, as Amro stated. — Cypress Frankenfeld
– Cypress Frankenfeld, Commented Aug 4, 2012 at 0:47

Amro · Accepted Answer · 2012-08-04 00:30:41Z

2

I've never used PBS before, but to run a MATLAB script from the shell, try the following:

matlab -nodesktop -nodisplay -r "addpath('/directory/path'); ga_opt_main; quit;"

where ga_opt_main.m is the name of the script file, and '/directory/path' is the directory where it resides. Note that you must have any other dependencies to this script on the MATLAB path as well.

There is also a convenient RUN function that does something similar:

matlab ... -r "run('/directory/path/ga_opt_main.m'); quit;"

edited Aug 4, 2012 at 0:30

answered Aug 4, 2012 at 0:25

Amro

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1 Comment

Nithya Subramanian Over a year ago

Thanks a lot. Yes, there was an error in the directory path command. Fixed it..Thanks again!

AGS · Accepted Answer · 2012-08-04 00:49:28Z

1

 ###############################
 #!/bin/sh
 #PBS -l nodes=1
 #PBS -l walltime=2:0:0
 #PBS -j oe
 #PBS -o localhost:/dev/null
 #PBS -d /your/working/directory


     cd $PBS_O_WORKDIR
     matlab -nodisplay -nodesktop -nojvm -nosplash -r "your_matlab_function"

I like to add addpath(genpath('~/your/script's/home')); to the actual matlab script/function. Also, do not add the ".m" to your matlab filename.

answered Aug 4, 2012 at 0:49

AGS

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