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 <n...@bx.psu.edu> wrote: > >>> > >>> 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. > >>> > > 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
