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

Alex Chekholko chekh at stanford.edu
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:
https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/MATLAB#example_single_matlab_file_run_via_qsub

Regards,
Alex

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 stanford.edu 347-401-4860



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