Hoffman2:Job Submission Templates: Difference between revisions

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[[Hoffman2|Back to all things Hoffman2]]
===Job submission templates===
===Job submission templates===
'''[[Hoffman2:Submit_job|Submit job]]'''
'''[[Hoffman2:Submit_job|Submit job]]'''

Revision as of 19:36, 29 November 2017

Back to all things Hoffman2

Job submission templates

Submit job

  • example script for submitting a single job

Submit job (tcsh)

  • same as above, written for tcsh

Submit jobarray

  • example script for submitting a jobarray with hard-coded array values

Submit jobarray (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. Copy the contents of the script template into a new script, e.g. myscript.sh. Watch out for line ending errors caused by copying/pasting from a Mac or PC. Line ending issues can be fixed with dos2unix myscript.sh.
  2. 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.
    • Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.
  3. Put your script content at the bottom.
  4. Submit directly to the job scheduler like this: qsub myscript.sh