- LICENSE AND COPYRIGHT
HPC::Runner::Slurm - Job Submission to Slurm
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.
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 the nodes from sinfo if not supplied
If the nodelist is supplied partition must be supplied
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.
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
<jillian.e.rowe at gmail.com>
Please report any bugs or feature requests to
bug-runner-init at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=HPC-Runner-Slurmm. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
You can find documentation for this module with the perldoc command.
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
AnnoCPAN: Annotated CPAN documentation
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.
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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