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gablab / mindhive

scripts, wiki and issues related to mindhive
mindhive.mit.edu
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exit status 139 on qsub? #26

Open liviaking opened 13 years ago

liviaking commented 13 years ago

I'm having some trouble submitting a matlab job to the queue. The command I use is:

/software/common/bin/ezsub -c "matlab -nodesktop -nosplash < /groups/vwfa/att_pilot/batch/PPI/runPPIFTWComplex.m" -n ftwrun

If I simply run matlab from command line: matlab -nodesktop -nosplash < /groups/vwfa/att_pilot/batch/PPI/runPPIFTWComplex.m

it runs fine, but whenever I submit it to the queue, it fails right away with exit status=139.

satra commented 13 years ago

i just ran:

ezsub -c "matlab -nodesktop -nosplash \< ~/test.m" -n foo

and it seems to work fine.

liviaking commented 13 years ago

Other scripts have worked for me in the past too, so I think it's at least somewhat script specific. The thing that confuses me though, is that when I run it just straight from the terminal, it doesn't crash.

satra commented 13 years ago

the job submission shouldn't crash. can you copy and paste the output from the job submission command.

liviaking commented 13 years ago

Command Line:

Jobfile: /users/kingl/pbs/ezsub_1322841361.579602.0.05.sh qsub -o /users/kingl/pbs -e /users/kingl/pbs /users/kingl/pbs/ ezsub_1322841361.579602.0.05.sh 782468.sub.mit.edu

PBS_ID 782468.sub.mit.edu

Email 1:

PBS Job Id: 782468.sub.mit.edu Job Name: ftwrun Exec host: ba6/0 Begun execution

Email 2:

PBS Job Id: 782468.sub.mit.edu Job Name: ftwrun Exec host: ba6/0 Execution terminated Exit_status=139 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00

Could it have something to do with the fact that the script generates figures on the screen? I think Jenny had some issues with that, but following her solution (setting DISPLAY to ba3.mit.edu:2.0) did not help in this case.

On Fri, Dec 2, 2011 at 10:53 AM, Satrajit Ghosh < reply@reply.github.com

wrote:

the job submission shouldn't crash. can you copy and paste the output from the job submission command.

Reply to this email directly or view it on GitHub: https://github.com/gablab/mindhive/issues/26#issuecomment-2991737

Note: Due to a typing injury, I use voice recognition for emails. While I proofread all my messages, mistakes still slip past more often than I'd like. I apologize and thank you for your patience.

Livia (Liwei) King Blackburne Graduate Student Brain and Cognitive Sciences, MIT

A Brain Scientist's Take on Creative Writing http://blog.liviablackburne.com