Hi Carsten,
I've been thinking a bit about this issue, and for now a relatively easy fix
would be to enable thread affinity when all cores on a machine are used. When
fewer threads are turned on, I don't want to turn on thread affinity because
any combination might either
- interfere with other
Hi,
FWIW, I have recently asked about this in the hwloc mailing list:
http://www.open-mpi.org/community/lists/hwloc-users/2010/10/0232.php
In general, hwloc is a useful tool for these things.
http://www.open-mpi.org/projects/hwloc/
Best,
Ondrej
On Thu, Oct 21, 2010 at 12:03, Carsten Kutzner
>>> Thanks for the information; the OpenMPI recommendation is probably because
>>> OpenMPI goes to great lengths trying to avoid process migration. The
>>> numactl doesn't prevent migration as far as I can tell: it controls where
>>> memory gets allocated if it's NUMA.
>> My understanding is t
On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote:
> On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
>
>>
>> Thanks for the information; the OpenMPI recommendation is probably because
>> OpenMPI goes to great lengths trying to avoid process migration. The numactl
>> doesn't prevent migration
On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
>
> Thanks for the information; the OpenMPI recommendation is probably because
> OpenMPI goes to great lengths trying to avoid process migration. The numactl
> doesn't prevent migration as far as I can tell: it controls where memory gets
> alloc
Thanks for the information; the OpenMPI recommendation is probably because
OpenMPI goes to great lengths trying to avoid process migration. The numactl
doesn't prevent migration as far as I can tell: it controls where memory gets
allocated if it's NUMA.
For gromacs the setting should of cours
Hi Sander,
On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote:
> Hi Carsten,
>
> As Berk noted, we haven't had problems on 24-core machines, but quite frankly
> I haven't looked at thread migration.
I did not have any problems on 32-core machines as well, only on 48-core ones.
>
> Currently, th
Hi Carsten,
As Berk noted, we haven't had problems on 24-core machines, but quite frankly I
haven't looked at thread migration.
Currently, the wait states actively yield to the scheduler, which is an
opportunity for the scheduler to re-assign threads to different cores. I could
set harder thr
Hi,
We haven't observed any problems running with threads over 24 core AMD nodes
(4x6 cores).
Berk
> From: ckut...@gwdg.de
> Date: Thu, 21 Oct 2010 12:03:00 +0200
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs
>
> Hi,
>
> does anyone have experie
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