Am 12.04.2012 um 11:11 schrieb Esztermann, Ansgar:
> This may be of limited value since we're using IntelMPI, not MVAPICH, but we
> did face similar problems. By default, iMPI would bind to cores 0..n-1, so
> multiple jobs on one host would step on each other's toes.
This will also happen then outside of SGE in case you use mpiexec just on the
command line - right?
Is each rank bound to a specific core, or just the the set of ranks to a set of
cores and the OS can place them inside this set as it likes?
> It is possible to disable the binding (I_MPI_PIN=disable), but that would
> also degrade performance badly (we have Magny-Cours CPUs).
Interesting, this would mean that the scheduler in the OS is not
operating/predicting in the best way.
-- Reuti
> Nowadays, we include this in our job scripts:
>
> $ -binding env linear:8
> PROC_LIST=${SGE_BINDING// /,}
> export I_MPI_PIN_PROCESSOR_LIST=${PROC_LIST%,}
>
> A.
>
> On Apr 11, 2012, at 16:11 , Dave Love wrote:
>
>> The gridengine binding (which gridengine keeps track of) separates jobs,
>> and it should be noticed by the MPI, which should then bind the
>> individual processes to the cores it's been given. I don't know
>> mvapich, but I know it uses hwloc, and should be able to do this
>> properly like openmpi does (modulo issues with recent hardware, sigh).
>> I thought mvapich would do the right thing automatically -- openmpi is
>> said often to look bad performance-wise by not doing core binding by
>> default.
>
> --
> Ansgar Esztermann
> DV-Systemadministration
> Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
>
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