NAME
HPC::Runner::PBS - Submit jobs to a PBS job scheduler.
DESCRIPTION
HPC::Runner::PBS is a wrapper around qsub and can be used to submit arbirtary bash commands to PBS.
It has two levels of management. The first is the main qsub command, and the second is the actual job, which runs commands in parallel, controlled by HPC::Runner::Threads or HPC::Runner::MCE.
It supports job dependencies. Put in the command 'wait' to tell PBS that some job or jobs depend on some other jobs completion. Put in the command 'newnode' to tell HPC::Runner::PBS to submit the job to a new node.
The only necessary option is the --infile, and --queue if you wish to run on a queue besides s48.
The bulk of this code is extended from HPC::Runner::Slurm.
queue
Same as the partition in HPC::Runner::Slurm
walltime
Define PBS walltime
mem
template_file
actual template file
One is generated here for you, but you can always supply your own with --template_file /path/to/template
SUBROUTINES/METHODS
run()
First sub called Calling system module load * does not work within a screen session!
submit_slurm()
Submit jobs to PBS using qsub
Uses almost the same logic as submit_slurm, so we'll keep that.
This subroutine was just about 100% from the following perlmonks discussions. All that I did was add in some logging.
http://www.perlmonks.org/?node_id=151886 You can use the script at the top to test the runner. Just download it, make it executable, and put it in the infile as
perl command.pl 1 perl command.pl 2 #so on and so forth
SYNOPSIS
use HPC::Runner::PBS;AUTHOR
Jillian Rowe <jillian.e.rowe@gmail.com>
Acknowledgements
This module was originally developed at and for NYU Abu Dhabi in the Center for Genomics and Systems Biology. With approval from NYUAD, this information was generalized and put on github, for which the authors would like to express their gratitude.
COPYRIGHT
Copyright 2015- Jillian Rowe
LICENSE
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.