Submit array jobs to a SGE cluster without all the suffering
Project description
psub
Submit array jobs without all the suffering
Stands for petko-submit, OG ernstlab member who came up with the idea.
New API (alpha):
There's a new (unstable) API that allows submitting jobs directly in Python.
Installation:
Must be installed under ~/utils like this:
mkdir ~/utils; cd ~/utils
git clone git@github.com:udincer/psub.git
Add alias:
# Optional: add psub as an alias
# Add the following to .bashrc
alias psub='/u/home/d/<your_username>/utils/psub/psub_main.sh '
How to use:
Make script containing each command you want to run in parallel in exactly one line:
# the_jobs.sh
python run_analysis.py theta1
python run_analysis.py theta2
python run_analysis.py theta3
python run_analysis.py theta4
python run_analysis.py theta5
Run psub like this, will batch 3 commands to one SGE job (for short jobs):
psub the_jobs.py 3
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