Hoffman2:Submit jobarray (readarray): Difference between revisions
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[[Hoffman2|Back to all things Hoffman2]] | [[Hoffman2|Back to all things Hoffman2]] | ||
In this example, subjects are read in from a subjects.txt file. subjects.txt is a text file with a single subject ID on each line. | In this example, subjects are read in from a subjects.txt file. subjects.txt is a text file with a single subject ID on each line. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix subjects.txt</code>. | ||
<nowiki>#!/bin/bash | <nowiki>#!/bin/bash | ||
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. /u/local/Modules/default/init/modules.sh | . /u/local/Modules/default/init/modules.sh | ||
module use /u/project/CCN/apps/modulefiles | module use /u/project/CCN/apps/modulefiles | ||
# Load the FSL module | |||
module load fsl | module load fsl | ||
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echo "This is subject ${subjects[$i]}" | echo "This is subject ${subjects[$i]}" | ||
# | # Your script content goes here...</nowiki> | ||
Latest revision as of 19:33, 29 November 2017
In this example, subjects are read in from a subjects.txt file. subjects.txt is a text file with a single subject ID on each line. Watch out for line ending errors caused by copying/pasting from a Mac or PC. Line ending issues can be fixed with dos2unix subjects.txt.
#!/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
# Load the FSL module
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]}"
# Your script content goes here...