NAME

BatchSystem::SBS - a Simple Batch System

DESCRIPTION

A light, file based batch system.

SYNOPSIS

a short example

#edit examples/sbsconfig-examples-1.xml to put your own local machines (it can be a good idea, if you have not a cluster, to enter your local machine with different addresses (localhost, 123.156.78.90, hostname) to see sommething a bit more realistic...

#System status #in a side term, to see every second the watch -n 1 ../scripts/sbs-scheduler-print.pl --config=sbsconfig-examples-1.xml

#to submit or dozen or so scripts on queue 'single'

../scripts/sbs-batch-submit.pl --config=sbsconfig-examples-1.xml --queue=single --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh

#and on a higher priority queue

../scripts/sbs-batch-submit.pl --config=sbsconfig-examples-1.xml --queue=single_high --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh --command=a.sh

#to update

../scripts/sbs-scheduler-update.pl --config=sbsconfig-examples-1.xml

#to check data consistency (and solve main problems

../scripts/sbs-scheduler-check.pl

#to remove a job --config=sbsconfig-examples-1.xml

../scripts/sbs-batch-remove --config=sbsconfig-examples-1.xml yourjobid

submiting command

You can submit either comman or scripts.

Script submited on a resource of type 'machine' will be sshed on the host

Once a resource is attributed to a job, the script is transformed, changing the following varaibles (see examples/*.sh)

$(machinefile} (for cluster type resource)

${nbmachines} (for cluster type resource)

${host} (for machine type resource)

${jobid}

At submition time, a directory with the job number (incremented integer) is created, where stdout/err will be written.

There will also have a batch.properties file (pids, start time etc. etc.)

EXPORT

FUNCTIONS

METHODS

my $sbs=BatchSystem::SBS->new();

Accessors

$sbs->scheduler

Returns the scheduler (BatchSystem::SBS::DefaultScheduler)

$sbs->workingDir([$val])

Get set the working directory

$sbs->

$sbs->

Actions

$sbs->job_submit(command=>cmd, queue=>queuename);

Returns a jobid

$sbs->job_remove(id=>job_id);

Remove the job from the list, the scheduler, kill processes

$sbs->job_action(id=>job_id, action=>ACTION);

Send an action to a job. ACTION can be of

'KILL': to kill (kill the process if running) one job

$sbs->job_infoStr(id=>job_id);

Returns a string (or undef if no job exist) with the job info

$sbs->job_info(id=>job_id);

Returns a hash (or undef if no job exist) with the job info

$sbs->jobs_dir([clean=>1]);

Get the job directory;

clean=>1 argument will clean the whole job directory

$sbs->jobs_list()

Returns an n x 4 array (each row contains jobid, queuename, scripts)

I/O

$sbs->readConfig(file=>file.xml)

Read its config from an xml file (see examples/ dir)

$sbs->dataRequest(request=>'req1,req2...')

request data (rpc oriented)

AUTHOR

Alexandre Masselot, <alexandre.masselot@genebio.com>

BUGS

Please report any bugs or feature requests to bug-batchsystem-sbs@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=BatchSystem-SBS. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

ACKNOWLEDGEMENTS

COPYRIGHT & LICENSE

Copyright (C) 2004-2007 Geneva Bioinformatics (www.genebio.com) & Jacques Colinge (Upper Austria University of Applied Science at Hagenberg)

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

cpanm BatchSystem::SBS

perl -MCPAN -e shell
install BatchSystem::SBS