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.

SEE ALSO

