[GE users] Default CPU core binding

reuti reuti at staff.uni-marburg.de
Mon Oct 4 11:58:08 BST 2010


Hi,

Am 04.10.2010 um 10:23 schrieb jewellc:

> Having just upgraded my installation of SGE to 6.2u5, I'm excited to see the new built-in core binding feature.  Currently, my installation (on Ubuntu 10.04, 8-core x86_64 nodes) uses a hacked version of the sge_cpuset system supplied in the Documents and Files section of the GE website, and a /usr/bin/cpuset utility that I wrote to use the Linux libcpuset library.  This is all well and good, but is a slightly untidy solution, and is not without its bugs (such as the cpuset.map file getting out of sync with what the scheduler thinks is a free slot).  The reason I do this is to prevent certain applications (eg multithreaded linear algebra packages such as ATLAS) from spawning threads all over an execution node and interfering with other jobs that are running on the same physical machine.  
> 
> 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 don't know what the "sge_cpuset" you used did in particular, but you can check here what the new feature supplies:

http://wikis.sun.com/display/gridengine62u5/Using+Job+to+Core+Binding

-- Reuti


> Thanks,
> 
> Chris
> 
> 
> --
> Dr Chris Jewell
> Department of Statistics
> University of Warwick
> Coventry
> CV4 7AL
> UK
> Tel: +44 (0)24 7615 0778
> 
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