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[farmshare-discuss] job submission to barley machines

Jason Bishop bishopj at stanford.edu
Tue Sep 25 08:57:07 PDT 2012


Hi Abhik, in general i would recommend taking off the -o and -e options from qsub so you can see what happens if the job doesn't run the way you expected.  for this particular case, i suspect that its not running because matlab isn't in the path.


try doing a module load MATLAB-XXXXXXX  at the top of the script (where XXXXX is the version you want and can be seen from module avail command).

jason


----- Original Message -----
From: "Abhik Lahiri" <alahiri at stanford.edu>
To: farmshare-discuss at lists.stanford.edu
Sent: Monday, September 24, 2012 8:26:55 PM
Subject: [farmshare-discuss] job submission to barley machines







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 

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