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
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