Assaf Gordon wrote:
> (moved to galaxy-dev)
> Nate Coraor wrote, On 06/02/2011 01:31 PM:
> > Peter Cock wrote:
> >> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <> wrote:
> >>>
> >>> 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.
> >>>
> Just a thought here:
> The actual parameters that are passed to the scheduler are not necessarily 
> hard-coded.
> Meaning, at least with SGE, specifying the number of cores can be:
>  qsub -pe threads=8
> or
>  qsub -pe cores=8
> or
>  qsub -pe jiffies=8
> and same thing for memory limitation (e.g. "-l virtual_free=800M").
> The reason is that those resources (e.g. "threads", "cores", "virtual_free") 
> are just identifiers, and they are created and configured by whomever 
> installed SGE - they are not built-in or hard-coded).
> So just be careful in your design/implementation when automatically 
> translating XML resources to hard-coded parameters.
> If you do hard-code them, just make sure the specifically document it (i.e. 
> Galaxy expect the SGE threads parameter to be "-pe threads=8" and nothing 
> else).

Hrm, I didn't realize that SGE didn't have a standard resource name for
this.  It's probably something we can just add into the XML as "cores"
in Galaxy == "threads" in my SGE install.

Thanks for the heads up.

> -gordon
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