Hoffman2:Submit jobarray (readarray): Difference between revisions
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[[Hoffman2|Back to all things Hoffman2]] | [[Hoffman2|Back to all things Hoffman2]] | ||
Note that subjects.txt is a text file with a single subject ID listed on each line. 'Watch out for line endings! Line ending issues can be fixed with <code>dos2unix</code>.' | Note that subjects.txt is a text file with a single subject ID listed on each line. '''Watch out for line endings! Line ending issues can be fixed with <code>dos2unix</code>.''' | ||
<nowiki>#!/bin/bash | <nowiki>#!/bin/bash |
Revision as of 22:23, 14 November 2017
Note that subjects.txt is a text file with a single subject ID listed on each line. Watch out for line endings! Line ending issues can be fixed with dos2unix
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#!/bin/bash #$ -cwd # error = Merged with joblog #$ -o joblog.$JOB_ID.$TASK_ID #$ -j y #$ -pe shared 2 #$ -l h_rt=8:00:00,h_data=4G # Email address to notify #$ -M $USER@mail # Notify when #$ -m a # Job array indexes #$ -t 1-16:1 # Load the job environment: . /u/local/Modules/default/init/modules.sh module use /u/project/CCN/apps/modulefiles module load fsl # This is optional # More info here: https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:FSL export NO_FSL_JOBS=true # Set up the subjects list readarray -t subjects < subjects.txt (( i=$SGE_TASK_ID - 1 )) echo "This is sub-job $SGE_TASK_ID" echo "This is subject ${subjects[$i]}" # Now do something with fsl, feat, etc. sleep 600