NAME

HPC::Runner::GnuParallel - Run arbitrary bash commands using GNU parallel. Can be used on its own or as a part of HPC::Runner::Slurm.

SYNOPSIS

  package Main;

  use Moose;

  extends 'HPC::Runner::GnuParallel';

  Main->new_with_options()->go;

  1;

Run straight as :

  cat stuff.cmd | parallelparser.pl | parallel --joblog `pwd`/runtasks.log --gnu -N 1 -q  gnuparallelrunner.pl --command `echo {}` --outdir `pwd`/gnulogs/ --seq {#}

  Where stuff.cmd is a file with the commands you need run.

  Or as a part or HPC::Runner::Slurm distro.

DESCRIPTION

HPC::Runner::GnuParallel is a part of a suite of tools to make HPC easy.

Attributes

using_gnuparallel

Indicate whether or not to use gnu parallel

infile

disable infile and read directly from the stream

go

Initialize MCE things and use HPC::Runner to parse and exec commands

parse_file_gnuparallel

Parse the file of commands and send each command off to the queue.

Acknowledgements

Before version 0.05

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 0.05:

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.

AUTHOR

Jillian Rowe <jillian.e.rowe@gmail.com>

COPYRIGHT

Copyright 2015- Weill Cornell Medical College in Qatar

LICENSE

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

SEE ALSO