[GE users] Default CPU core binding

jewellc chris.jewell at warwick.ac.uk
Mon Oct 4 12:53:56 BST 2010


>> Is it possible to set the new core binding feature to automagically use CPU affinity to achieve the same effect? Can I set up my Grid Engine installation to automatically assign a process to only the cores that have been requested in the qsub (or qlogin) command?

> this is the reason, why I prefer using the non-threaded versions of ATLAS or ACML. If they are not prepared to do it, you don't have to set it up in the queueing system (unless this is exactly the parallelization you want to use for your application of course).

I'm trying to make my system easy for inexperienced users by providing the parallel BLAS libraries.  Users simply choose how many CPUs they want to use, and the system allocates their job to an SMP parallel environment.

> I don't know what the "sge_cpuset" you used did in particular, but you can check here what the new feature supplies:

the sge_cpuset suite essentially consists of job prolog, starter, and epilog scripts.  The prolog sets up a "cpuset" on the machine, which essentially attaches the sge_shepherd and all sub-processes to a fixed set of CPUs.  Thus, even if the user's job spawns multiple threads, they are contained inside the cpuset and do not interfere with other jobs running on the same host.  I think this is a really useful feature, since it essentially provides a 'virtual' environment without the startup and runtime overheads of a full-blown virtual machine.  I would encourage the SGE Developers to perhaps explore this avenue a little further....

As a philosophical point, modern HPC seems to require a mix of multithreading and message passing, so addressing the issue of how to prevent jobs interfering with each other on SMP (or NUMA) machines seems really important.  I wonder whether I could ask other readers of this list to share their experiences of controlling other multithreaded applications within the multi-core scheduled environment?



Dr Chris Jewell
Department of Statistics
University of Warwick
Tel: +44 (0)24 7615 0778


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