NAME
HPC::Runner::Slurm - Job Submission to Slurm
SYNOPSIS
Please see the indepth documentation at HPC::Runner::Usage.
package Main;
extends 'HPC::Runner::Slurm';
Main->new_with_options(infile => '/path/to/commands');
This module is a wrapper around sbatch and can be used to submit
arbirtary bash commands to slurm.
It has two levels of management. The first is the main sbatch 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 slurm
that some job or jobs depend on some other jobs completion. Put in the
command 'newnode' to tell HPC::Runner::Slurm to submit the job to a new
node.
The only necessary option is the --infile.
Submit Script
cmd1
cmd2 && cmd3
cmd4 \
--option cmd4 \
#Tell HPC::Runner::Slurm to put in some job dependencies.
wait
cmd5
#Tell HPC::Runner::Slurm to pass things off to a new node, but this job doesn't depend on the previous
newnode
cmd6
get_nodes
Get the nodes from sinfo if not supplied
If the nodelist is supplied partition must be supplied
submit_slurm()
Submit jobs to slurm queue using sbatch.
This subroutine was just about 100% from the following perlmonks
discussions. All that I did was add in some logging.
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
AUTHOR
Jillian Rowe, <jillian.e.rowe at gmail.com>
BUGS
Please report any bugs or feature requests to bug-runner-init at
rt.cpan.org, or through the web interface at
will be notified, and then you'll automatically be notified of progress
on your bug as I make changes.
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc HPC::Runner::Slurm
You can also look for information at:
* RT: CPAN's request tracker (report bugs here)
* AnnoCPAN: Annotated CPAN documentation
* CPAN Ratings
* Search CPAN
Acknowledgements
Before Version 2.41
This module was originally developed at and for Weill Cornell Medical
College in Qatar within ITS Advanced Computing Team. With approval from
WCMC-Q, this information was generalized and put on github, for which
the authors would like to express their gratitude.
As of Version 2.41:
This modules continuing development is supported by NYU Abu Dhabi in
the Center for Genomics and Systems Biology. With approval from NYUAD,
this information was generalized and put on bitbucket, for which the
authors would like to express their gratitude.
LICENSE AND COPYRIGHT
Copyright 2014 Weill Cornell Medical College in Qatar.
This program is free software; you can redistribute it and/or modify it
under the terms of the the Artistic License (2.0). You may obtain a
copy of the full license at:
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Versions is governed by this Artistic License. By using, modifying or
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This license includes the non-exclusive, worldwide, free-of-charge
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