Hi, Just add some info about this, I have attempted to do so on SGE cluster.
I found that $NSLOTS works only for MPI jobs as it's part of the MPI integration in SGE. Other non MPI jobs won't work. For example: python parallel_groomer.py input output $NSLOTS, $NSLOTS won't be replaced by the SGE with the specified number. Regards, Derrick On Sat, Jun 16, 2012 at 1:52 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Fri, Jun 15, 2012 at 4:38 PM, James Taylor <ja...@jamestaylor.org> > wrote: > > This is exactly what I think we should do (and have for a long time), > but I > > think the variable should be something like: > > > > GALAXY_CPUS > > > > (threads is not accurate, a multithread or multiprocess job might want > to use > > this info, something even more abstract than CPUS might make sense, but > > SLOTS has never made sense to me). > > I agree that a Galaxy specific name makes a lot of sense, and that > the SGE term "slots" is a bit odd. Using CPUS however is potentially > ambiguous with CPUs vs cores - my desktop has two quad core CPUs, > i.e. 2 CPUs but 8 cores. > > Where do you think this number should come from? A new entry in the > runner URL is simple albeit potentially redundant with cluster-specific > entries in the runner URL. As to the alternative (doing it automatically), > for PBS and SGE determining the number of cores from the cluster > configuration and/or parsing the cluster runner URL sounds doable - > what about the other backends? > > Peter > ___________________________________________________________ > 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/ >
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