Hoffman2:Job Submission Templates

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Revision as of 22:50, 14 November 2017 by Dmargolis (talk | contribs)
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Submit job example

  • example script for submitting a single job
  • Submit job example (tcsh)
    • same as above, written for tcsh
  • Submit jobarray example
    • example script for submitting a jobarray with hard-coded array values
  • Submit jobarray example (readarray)
    • example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'

To work with these example scripts:

  1. Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt). You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.
  2. Put your script content at the bottom.
  3. Submit directly to the job scheduler like this: qsub myscript.sh