Am 12.11.2014 um 00:09 schrieb Christopher Heiny: > On 11/10/2014 11:21 PM, Reuti wrote: >> Am 11.11.2014 um 06:37 schrieb Christopher Heiny: >> >>> Hi all, >>> >>> We're running OGS 2011.11p1, with a 1:1 slot:core mapping. We mostly run >>> submit single threaded array jobs, one slot per task. We now want to >>> multi-thread some of the programs in order to speed up processing, but need >>> a way to allocate <n> slots to an <n> threaded task. >>> >>> The first idea was to use a parallel environment to manage this, but since >>> the jobs are all with script (rather than a binary), we got bitten by this >>> bug: >>> http://gridengine.org/pipermail/dev/2011-December/000081.html >> >> Nevertheless you can submit the jobscript as binary, it might be necessary >> to specify the complete path to the script though. > > If you do that, GE will ignore all the #$ escapes in the script.
That's true. An elaborate task could be to write a JSV to read the file and add all the extra SGE options found therein to the submission command, hence no change for the user. -- Reuti > However, it would probably be fairly quick to write a Python wrapper that > extracts all the escapes, and the builds/executes a qsub command line. > > I'll let you know how it goes. > > Thanks! > Chris > >> >> -- Reuti >> >> >>> Unfortunately, patching/updating the GE software is not an option at the >>> moment. We've got to wait a few months for that, and in the meantime we >>> need a workaround for slot allocation. >>> >>> Currently, I'm thinking of using a consumable equal to the number of >>> slots/cores on a machine to control allocation. I *think* this will work >>> OK as an interim solution. What I was wondering was: has anyone >>> encountered a similar situation? Did you use this trick to work around it? >>> Or is there a better workaround? >>> >>> Thanks very much! >>> Chris >>> _______________________________________________ >>> users mailing list >>> users@gridengine.org >>> https://gridengine.org/mailman/listinfo/users >> > _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
