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[farmshare-discuss] matlab was:Re: job submission to barley machines

Alex Chekholko chekh at
Mon Sep 24 21:07:17 PDT 2012

Hi Abhik,

Which matlab are you using?

I recommend the following:
1) use 'module load MATLAB-MATLAB-R2012a'
2) use the '-V' flag for qsub to pass the environment along

I updated the example here:


On 9/24/12 8:26 PM, Abhik Lahiri wrote:
> Hi,
> I am trying to submit bash scripts as jobs to the barley machines. The
> command I am using is: qsub -cwd -o /dev/null -e /dev/null job1.script
> However, none of my jobs run. They script runs for a few seconds before
> getting killed, and nothing is written to the output file in my script
> too (I had earlier put filenames for the -o and -e but both the stdout
> and stderr files were empty).
> My shell script starts matlab and runs a matlab script (the command used
> is something like - unset DISPLAY; matlab > output_file << EOF;
> matlab_task(arg1, arg2); exit; EOF - so, its the usual script to run a
> matlab task and write the output to a file output_file). To debug this,
> I ran a test job by ssh'ing directly into a barley and running this same
> script, and it runs fine!!
> So, I wonder why the job scheduler is not able to run the script? Are
> there some mandatory parameters I need to pass along with the qsub
> command that I am missing here? The qsub command is run from my home dir
> in /mnt/glusterfs, and output_file (in the matlab command above) is also
> in my home dir in /mnt/glusterfs, so I am following the guidelines about
> the location of input/output scripts here.
> Any help from someone will be greatly appreciated!! My research is on
> hold right now because of this problem :(
> Thanks!
> Abhik

Alex Chekholko chekh at 347-401-4860

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