bash-parallel
Only talking about parallel_submit_legacyV1.1.sh, other scripts are depreciated Purpose: bash script to submit commands/other scripts in parallel
Prerequisites: Tested mainly on MAC OSX, some testing on Ubuntu 14.04 LTS
Parameters: Mandatory -s The script you wish to run (write it out like how you would normally write it on the commandline) -j the maximum number of jobs you want to run cocurrently Optional -c deletes the intermediate .txt files (only useful for debugging) -m Try not to let free memory dip below this number (in kilobytes), takes precedence over the -j flag, but the -j flag still needs to be set
Notes about usage: The objects/inputs you wish to run cocurrently must be specified in a .parallel file. For example, if I needed processing to be completed on subjects 1001.nii.gz, 1002.nii.gz, and 1003.nii.gz, I would make a file named subs.parallel and if I were to call cat subs.parallel I would see as output: 1001.nii.gz 1002.nii.gz 1003.nii.gz
Example usage: parallel_submit_legacyV1.1.sh -s "MBA.sh -s sub_MPRAGES.parallel -o /Volumes/VossLab/Repositories/Bike/FIRST_practice -a /Volumes/VossLab/Repositories/MBA_maps -b /Volumes/VossLab/Repositories/MBA_maps/brainPrior/Ave_brain.nii.gz" -j 8
For more help see the top part of the parallel_submit_legacyV1.1.sh script.