Hi, Am 29.04.2013 um 10:00 schrieb [email protected]:
> we have parallel jobs with mixture openmp and mpi compiled with ifort. We > found out that job threads change the physical processor core from time to > time, this can lead to increased run time of the job. Outside the gridengine > there is a variable "export KMP_AFFINITY=scatter " which set affinity to > physical cores of the threads. > Unfortunately we can not use this setting in our gridengine job scripts. With > this definition two different jobs which are submitted to the same node will > occupy the same processor cores > by the gridengine. > Does anyone know a way to define this option in the gridengine directly ? I'm > using ogs 2011.11p1 on Intel 6core processors. With 6 cores per machine I would simply request full nodes. AFAIK the commercial GridEngine from Univa contains extensions to monitor granted cores on a host level, so that each of such a job could be given an unique list of cores. If any KMP_... variable would allow a syntax to accept a list of cores, it should work that your executable can make a proper allocation. But such a thing is not available in the open source version. What might work: define one queue per core with only one slot. Hence you will get many different queues per node for a parallel job and from the $PE_HOSTFILE you know which cores can be used where. -- Reuti _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
