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.cock@googlemail.com> wrote:
On Fri, Jun 15, 2012 at 4:38 PM, James Taylor <james@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
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