File Coverage

blib/lib/HPC/Runner/GnuParallel.pm

Criterion	Covered	Total	%
statement	9	24	37.5
branch			n/a
condition			n/a
subroutine	3	5	60.0
pod			n/a
total	12	29	41.3

#!/usr/bin/env perl

package HPC::Runner::GnuParallel;

our $VERSION = '0.04';

use DateTime;
use DateTime::Format::Duration;

use Moose;
extends 'HPC::Runner';
extends 'HPC::Runner::MCE';

with 'MooseX::Getopt';
with 'MooseX::Getopt::Usage';
with 'MooseX::Getopt::Usage::Role::Man';

=encoding utf-8

=head1 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.

=head1 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/

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

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


=head1 DESCRIPTION

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

=head1 Attributes

=head2 using_gnuparallel

Indicate whether or not to use gnu parallel

=cut

has 'using_gnuparallel' => (
    is => 'rw',
    isa => 'Bool',
    default => 1,
    required => 0,
);

=head2 infile

disable infile and read directly from the stream

=cut

has '+infile' => (
    required => 0,
);

has 'command' => (
    required => 1,
    isa => 'Str',
    is => 'rw',
);


=head2 go

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

=cut

sub go{
    my $self = shift;

    my $dt1 = DateTime->now();

    $self->logname('gnuparallel');

#    $self->prepend_logfile("MAIN_");
#    $self->log($self->init_log);

    $self->parse_file_gnuparallel;

    $DB::single=2;

    my $dt2 = DateTime->now();
    my $duration = $dt2 - $dt1;
    my $format = DateTime::Format::Duration->new(
        pattern => '%Y years, %m months, %e days, %H hours, %M minutes, %S seconds'
    );

#    $self->log->info("Total execution time ".$format->format_duration($duration));
    return;
}

=head2 parse_file_gnuparallel

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

=cut

sub parse_file_gnuparallel{
    my $self = shift;

    $self->cmd($self->command);

    $DB::single=2;

#    $self->log->info("Enqueuing command:\n".$self->cmd);
    $self->run_command_mce;
    $self->clear_cmd;
    $self->inc_counter;
}


1;

__END__


=head1 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.

=head1 AUTHOR

Jillian Rowe E<lt>[e-mail]<gt>

=head1 COPYRIGHT

Copyright 2015- Weill Cornell Medical College in Qatar

=head1 LICENSE

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

=head1 SEE ALSO

=cut