On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Peter Cock wrote:
> On a related point, I've previously suggested a $variable could be defined
> for use in tool XML wrappers to set the number of threads. This number
> could come from a general configuration file, or perhaps via the cluster
> settings - the point is the tool doesn't need to know, it just gets told how
> many threads it is allowed.
Yeah, that's the idea.
job_conf.xml:
<?xml version="1.0"?>
<job_conf>
<destinations>
<destination name="default" runner="local"/>
<destination name="pbs_default" runner="pbs">
<native_param name="queue">batch</native_param>
</destination>
</destinations>
<tools>
<tool id="upload1" destination="default"/>
<tool id="bowtie_wrapper" destination="pbs_default">
<resource type="cores">8</resource>
</tool>
</tools>
</job_conf>
pbs.py then knows to translate '<resource
type="cores">8</resource>' to
'-l nodes=1:ppn=8'.
Your tool can access that value a bunch, like $__resources__.cores.
The same should be possible for other consumables.
Sounds good. Would there be a global default setting somewhere in
universe.ini or elsewhere for when job_conf.xml didn't set a value?
Peter