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[farmshare-discuss] How to submit batch jobs on barley?

Ken Van Tilburg kenvt at stanford.edu
Tue Mar 6 15:29:52 PST 2012


Hi,

My collaborators and I at the Stanford Physics department have a few
CPU-intensive simulations to run (with a program called Madgraph), and
would like to use the CPUs atbarley.stanford.edu if possible.  However, I
had some trouble running batch jobs.

I made an account on corn-image-new.stanford.edu, so I now have a folder
/mnt/glusterfs/kenvt/.  I have an executable that runs fine in that folder
with the command:
"./bin/generate_events 0 run1"
In other words, it takes two arguments, an integer ("0") and a string
("run1") and automatically outputs text data in some other folder.

How would I submit this to the batch queue with the command "qsub"?  I know
you cannot submit an executable with "qsub", so I tried running a script
that executes this "generate_events" executable, but when I type "qstat -j
<JOBID>", I get a bunch of output that says the job was never queued up
because all the clusters were overloaded/full.

Would you be able to offer any advice on how to submit these jobs in batch
form?  What would the script and the qsub command need to look like?  We
have about 50 jobs that take a few hours each to run.

Thank you in advance,
Ken Van Tilburg
PS: Sorry if this is not the right channel to ask for help.
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