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I am trying to submit a job via bsub linux utility using this bash script titple launchparse.sh:

#!/bin/bash

#BSUB -W 80:0
#BSUB -R rusage[mem=4000]
#BSUB -J "myarray[101-150]"
filenumber=$(($LSB_JOBINDEX*100000))
java -cp ./ejml-0.19-nogui.jar:./ejml-0.19-src.zip:./stanford-parser-3.2.0-javadoc.jar:./stanford-parser-3.2.0-models.jar:./stanford-parser-3.2.0-sources.jar:./stanford-parser.jar:. Pubmedparse $filenumber.txt done$filenumber

However, whenever I check to see if the jobs have been submitted using bjobs -a , I get that my jobs have been exited. Can anyone see what is wrong with the syntax of

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I think your script is fine. If I replace the java command line with

echo XXX > /tmp/done$filenumber

then it works. Its probably the java process that is exiting with a non zero exit code. Try redirecting the stdout/stderr and exit code of the java process to a file, or use the bsub options -o/-oo/-e/-eo.

For the jobs you submitted already, bjobs -l <jobid> will show you the exact exit code. For example,

Mon Feb  3 15:00:02: Exited with exit code 1. The CPU time used is 0.0 seconds.
  • Your post will probably be removed: it's not an answer. It creates unnecessary work to deal with. – suspectus Feb 3 '14 at 21:19
  • Hi @suspectus. I agree that my post isn't an answer, but it is helpful. Redirecting the stdout/err will help kolonel determine why his job is going to exit status. Can you suggest how I should provide this information? – Michael Closson Feb 3 '14 at 21:22
  • I guess we can let this stay. Michael, if you're affirmative in your answer, and if it helps the OP solve their problem, then by all means it's an answer. Just don't add "I would have posted a comment" or something like that. – slhck Feb 4 '14 at 7:46

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