Yep, we had to do this too, before upgrading to a GE release (UGE, in our case) that supports cgroups. cgroups allow you to limit on actual physical pages used by a job, rather than address space request like h_vmem.
On Thu, Jun 02, 2016 at 05:25:30PM +0200, Julien Nicoulaud wrote: > I have had issues in the past with Java jobs and h_vmem. When using a large > initial heap size, SGE would kill the java process at startup when it is > allocating its memory. You may want to lookup the MALLOC_ARENA_MAX > environment variable. > > We ended up using s_vmem instead, and handling it in our job scripts. > > 2016-05-09 18:31 GMT+02:00 Alex Chekholko <ch...@stanford.edu>: > > > IIRC this bug had to do with setting your "consumable" value to "YES" vs > > "JOB". I think it only affected you if you have your consumable value per > > job instead of per slot. > > > > I have now: > > > > #name shortcut type relop requestable consumable > > default urgency > > > > h_vmem h_vmem MEMORY <= YES YES 1G 0 > > > > We used to use "JOB" in that consumable column. > > > > > > On 05/09/2016 02:13 AM, nico.faer...@id.unibe.ch wrote: > > > >> Hi, > >> > >> We are running OGS/GE 2011.11p1. Concerning the problem that for certain > >> multi-core jobs the reported h_vmem value is much higher than the true > >> amount of memory used by the job, can anyone propose a solution to this > >> problem, e.g. working patch, ??? How do you deal with this problem? We > >> want to keep h_vmem consumable to prevent jobs from overbooking a node. > >> > >> Thank you, > >> Nico > >> > >> > >> _______________________________________________ > >> users mailing list > >> users@gridengine.org > >> https://gridengine.org/mailman/listinfo/users > >> > >> > > -- > > Alex Chekholko ch...@stanford.edu > > > > _______________________________________________ > > users mailing list > > users@gridengine.org > > https://gridengine.org/mailman/listinfo/users > > > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users -- -- Skylar Thompson (skyl...@u.washington.edu) -- Genome Sciences Department, System Administrator -- Foege Building S046, (206)-685-7354 -- University of Washington School of Medicine _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
