HPC::Runner::Slurm(3)

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.

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

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 <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.

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)

    <http://rt.cpan.org/NoAuth/Bugs.html?Dist=HPC-Runner-Slurm>

•   AnnoCPAN: Annotated CPAN documentation

    <http://annocpan.org/dist/HPC-Runner-Slurm>

•   CPAN Ratings

    <http://cpanratings.perl.org/d/HPC-Runner-Slurm>

•   Search CPAN

    <http://search.cpan.org/dist/HPC-Runner-Slurm/>

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:

<http://www.perlfoundation.org/artistic_license_2_0>

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

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