NAME

    HPC::Runner - HPC Runner::Slurm, Runner::MCE and Runner::Threads base
    class

VERSION

    Version 0.01

SYNOPSIS

    This is a base class for HPC::Runner::MCE and HPC::Runner:Threads. You
    should not need to call this module directly.

EXPORT

VARIABLES

 infile

    File of commands separated by newline. The command 'wait' indicates all
    previous commands should finish before starting the next one.

 _set_infile

    Internal variable

 outdir

    Directory to write out files and logs.

 _set_outdir

    Internal variable

 logdir

    Pattern to use to write out logs directory. Defaults to
    outdir/prunner_current_date_time/log1 .. log2 .. log3.

 procs

    Total number of running children allowed at any time. Defaults to 10.
    The command 'wait' can be used to have a variable number of children
    running. It is best to wrap this script in a slurm job to not overuse
    resources. This isn't used within this module, but passed off to
    mcerunner/parallelrunner.

 job_scheduler_id

    Job Scheduler ID running the script. Passed to slurm for mail
    information

Internal VARIABLES

    You shouldn't be calling these directly.

 jobref

    Array of arrays details slurm/process/scheduler job id. Index -1 is the
    most recent job submissisions, and there will be an index -2 if there
    are any job dependencies

 wait

    Boolean value indicates any job dependencies

Subroutines

 set_logdir

    Set the log directory

 set_logfile

    Set logfile

 init_log

    Initialize Log4perl log

 run_command_threads

    Start the thread, run the command, and finish the thread

 run_command_mce

    MCE knows which subcommand to use from Runner/MCE - object mce

 _log_commands

    Log the commands run them. Cat stdout/err with IO::Select so we
    hopefully don't break things.

    This example was just about 100% from the following perlmonks
    discussions.

    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=Runner-Init. 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 Runner::Init

    You can also look for information at:

      * RT: CPAN's request tracker (report bugs here)

      http://rt.cpan.org/NoAuth/Bugs.html?Dist=Runner-Init

      * AnnoCPAN: Annotated CPAN documentation

      http://annocpan.org/dist/Runner-Init

      * CPAN Ratings

      http://cpanratings.perl.org/d/Runner-Init

      * Search CPAN

      http://search.cpan.org/dist/Runner-Init/

Acknowledgements

    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.

LICENSE AND COPYRIGHT

    Copyright 2014 Weill Cornell Medical College.

    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.

    Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER
    AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES.
    THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
    PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY
    YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR
    CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
    CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
    EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

