Peter Cock wrote:
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?
default_cluster_job_runner will remain for backwards compatibility, but
we'll ship a sample job_conf.xml that runs everything locally by
default.
--nate
Peter