On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <n...@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?


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