Hoffman2:Job Submission Templates: Difference between revisions
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#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. | ||
#*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. | #Put your script content at the bottom. | ||
#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code> | #Submit directly to the job scheduler like this: <code>qsub myscript.sh</code> | ||
Revision as of 19:23, 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
- 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