Peter Cock wrote:
On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <nate(a)bx.psu.edu>
> 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
>> many threads it is allowed.
> Yeah, that's the idea.
> <?xml version="1.0"?>
> <destination name="default" runner="local"/>
> <destination name="pbs_default" runner="pbs">
> <native_param name="queue">batch</native_param>
> <tool id="upload1" destination="default"/>
> <tool id="bowtie_wrapper"
> <resource type="cores">8</resource>
> pbs.py then knows to translate '<resource
> '-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