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.\" ========================================================================
.\"
.IX Title "PMP::pbs 3"
.TH PMP::pbs 3 "2013-01-31" "perl v5.10.1" "User Contributed Perl Documentation"
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.SH "NAME"
PMP::pbs \- a subclass of PMP for batched processing.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
See the \s-1PMP\s0 documentation for a cogent synopsis.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A subclass of \s-1PMP\s0, it uses the Portable Batch System to submit its
jobs. The advantage of course is that stages that do not depend on
each other can be executed in parallel. Naturally requires \s-1PBS\s0 to be
installed on the system.
.SH "OVERVIEW"
.IX Header "OVERVIEW"
PMP::pbs is used exactly like its superclass \s-1PMP\s0. There are three
additional methods, setCommand, setQueue and setHosts, for setting 
the batch command, the batch queue and the batch hosts respectively. 
In terms of implementation all that PMP::pbs does is overwrite the 
execStage method of \s-1PMP\s0. See the \s-1PMP\s0 documentation for all the gory 
details.
.SH "METHODS"
.IX Header "METHODS"
.SS "setCommand"
.IX Subsection "setCommand"
Sets the batch command to use (qsub or msub).
.SS "setQueue"
.IX Subsection "setQueue"
Sets the batch queue to use (medium, short, or long).
.SS "setHosts"
.IX Subsection "setHosts"
Sets the batch hosts to use (colon separated list, i.e. \*(L"yorick:bullcalf\*(R").
.SS "setPriorityScheme"
.IX Subsection "setPriorityScheme"
Sets the job priority scheme to use. The only one currently
implemented is \*(L"later-stages\*(R", which gives priority to stages further
down the dependency list. This has the effect of trying to finish
individual pipelines before starting on the next pipeline. The default
is to use no ordering.