/ 
HPC-Runner-2.48
River stage one • 4 direct dependents • 5 total dependents
/ HPC::Runner

NAME

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

VERSION

Version 2.4.2

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.

Internal VARIABLES

You shouldn't be calling these directly.

wait

Boolean value indicates any job dependencies

process_table

We also want to write all cmds and exit codes to a table

plugins

Load plugins

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

Subroutines

set_logdir

Set the log directory

set_logfile

Set logfile

init_log

Initialize Log4perl log

process_plugins

Split and process plugins

run_command_threads

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

_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=HPC-Runner. 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

You can also look for information at:

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.