[GE dev] Core binding suggestion...

jewellc chris.jewell at warwick.ac.uk
Wed Oct 6 16:42:15 BST 2010

On 6 Oct 2010, at 15:50, Daniel Templeton wrote:

> I forgot to mention that you can use "-binding pe linear:1", which tells OGE not to do the processor binding itself, but instead to pass along the info to the job's MPI via env vars.

Interestingly, I see that when I a "qsub -pe mpi 8 -binding pe linear:1  myScript.com" with my mpi parallel environment (alloc rule $round_robin), my pe_hostfile looks like this:

exec3 2 batch.q at exec3.cluster.stats.local 0,0
exec2 1 batch.q at exec2.cluster.stats.local 0,0
exec7 1 batch.q at exec7.cluster.stats.local 0,0
exec5 1 batch.q at exec5.cluster.stats.local 0,0
exec1 1 batch.q at exec1.cluster.stats.local 0,0
exec4 1 batch.q at exec4.cluster.stats.local 0,0
exec6 1 batch.q at exec6.cluster.stats.local 0,0

In other words, for my 8 processor MPI job, exec3 is assigned 2 slots, but if my MPI subsystem (OpenMPI, FYI) were aware of the suggested binding, it might result in both processes being bound to socket 0, core 0.  Is this expected behaviour?  Shouldn't the binding on exec3 be "0,0:0,1" ?


(PS Is it useful to be asking this on the dev list, or shall I jump to the user list?)
Dr Chris Jewell
Department of Statistics
University of Warwick
Tel: +44 (0)24 7615 0778


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