In theory GALAXY_SLOTS is now always set unless Galaxy is pretty old - I still think it is important for tools to specify defaults using the \${GALAXY_SLOTS:-4} idiom so that tools themselves don't have explicit dependencies on the Galaxy runtime and in case new resource managers or job runners come along that don't set this. That said - I figured someday someone would ask this question so there is indeed undocumented magic to determine if the number of slots has been configured explicitly to 1 or if that is just the fallback because it was left unspecified or Galaxy didn't know how to determine it from the resource manager. The magic environment variable is GALAXY_SLOTS_CONFIGURED - if that is set and GALAXY_SLOTS is 1 - Galaxy believes that the number of requested cores is truly and explicitly 1. If GALAXY_SLOTS is 1 and GALAXY_SLOTS_CONFIGURED is not set - Galaxy is just supplying the default of 1 to the tool because it doesn't know what else to do. (1 is used by the local runner if local_slots is not set i job_conf or used by all the other job runners if they cannot figure out what the environment is requesting). I don't know how actionable it is from a tool author perspective - but I did think it was important to track it. Hope this helps. -John On Fri, Oct 17, 2014 at 5:19 AM, Gildas Le Corguille <lecorguille@sb-roscoff.fr> wrote:
Hi,
I'm not sure to understand ... I was but not now anymore :P
When you find \${GALAXY_SLOTS:-4} in a wrapper, and if you haven't set a tool_runner (-pe thread 8) for this tool, by default it will use 4 splots ! No ?
Is there a global GALAXY_SLOTS variable ?
Thanks
Gildas
Le 17/10/2014 02:03, Björn Grüning a écrit :
Hi Wolfgang,
\${GALAXY_SLOTS:-4} in this case will default to 4 if you have not configured it in job_conf.xml. Otherwise yes, it will be 1.
Ciao, Bjoern
Am 17.10.2014 um 00:05 schrieb Wolfgang Maier:
Hi,
this is just to make sure: the GALAXY_SLOTS environmental variable set by Galaxy when running tools will always be a number >= 1 with 1 being the default if nothing else is configured in the job runner settings ?
Correct ?
Thanks, Wolfgang
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