Hoffman2:Job Submission Templates: Difference between revisions
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===To work with these example scripts=== | ===To work with these example scripts=== | ||
#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for non-Linux (Mac or PC) line endings.''' Line ending issues can be fixed with <code>dos2unix</code>. | #Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for non-Linux (Mac or PC) line endings.''' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>. | ||
#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt). | #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. | #*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. |
Revision as of 19:25, 29 November 2017
Job submission templates
- example script for submitting a single job
- same as above, written for tcsh
- example script for submitting a jobarray with hard-coded array values
- example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'
To work with these example scripts
- Copy the contents of the script template into a new script, e.g.
myscript.sh
. Watch out for non-Linux (Mac or PC) line endings. Line ending issues can be fixed withdos2unix myscript.sh
. - 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.
- Put your script content at the bottom.
- Submit directly to the job scheduler like this:
qsub myscript.sh