contribs/arrayrun/arrayrun

#!/bin/bash
### Simulate an array job
### $Id: arrayrun,v 1.6 2011/02/10 11:57:53 root Exp $

### Copyright 2009,2010 Bjørn-Helge Mevik <b.h.mevik@usit.uio.no>
###
### This program is free software; you can redistribute it and/or modify
### it under the terms of the GNU General Public License version 2 as
### published by the Free Software Foundation.
###
### This program is distributed in the hope that it will be useful,
### but WITHOUT ANY WARRANTY; without even the implied warranty of
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
### GNU General Public License version 2 for more details.
###
### A copy of the GPL v. 2 text is available here:
### http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt


## Debugging
#set -x

### Configuration:
## The work horse:
WORKER=/site/lib/arrayrun_worker

## Documentation:
function usage () {
    echo "Run many instances of the same job or command in the queue system.
The instances are submitted via sbatch, and each get their own value
of the environment variable TASK_ID.  This can be used to select which
intput or output file to use, etc.

Usage:
 arrayrun [-r] taskids [sbatch arguments] command [arguments]
 arrayrun [-h | --help]

Arguments:
 '-r':         Restart a job if it fails.  For security reasons, each job is
               restarted only once, and no more than 5 jobs will be restarted.
 'taskids':    Run 'command' with TASK_ID set to the values specified in
               'taskids'.  'taskids' is a comma separated list of integers,
               ranges of integers (first-last) or ranges with step size
               (first-last:step).  For instance
                 1-5 means 1, 2, 3, 4, 5
                 1,4,6 means 1, 4, 6
                 10-20:5 means 10, 15, 20
                 1-5,15,100-150:25 means 1, 2, 3, 4, 5, 15, 100, 125, 150
               Note: spaces, negative number or decimal numbers are not allowed.
 'sbatch arguments': Any command line arguments for the implied sbatch.  This
               is most useful when 'command' is not a job script.
 'command':    The command or job script to run.  If it is a job script, it can
               contain #SBATCH lines in addition to or instead of the 'sbatch
               arguments'.
 'arguments':  Any arguments for 'command'.
 '-h', '--help' (or no arguments): Display this help."
}

if [ $# == 0 -o "$1" == '--help' -o "$1" == '-h' ]; then
    usage
    exit 0
fi

if [ -n "$SLURM_JOB_ID" ]; then
    ## Started in a job script.  Run with srun to make "scancel" work
    exec srun --ntasks=1 $WORKER "$@"
else
    exec $WORKER "$@"
fi