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