[gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Sander Pronk pronk at cbr.su.se
Thu Oct 21 12:27:17 CEST 2010

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 thread affinity but that could compromise system responsiveness (when running mdrun on a desktop machine without active yielding, the system slows down noticeably). 

One thing you could try is to turn on the THREAD_MPI_WAIT_FOR_NO_ONE option in cmake. That turns off the yielding which might change the migration behavior.

BTW What do you mean with bad performance, and how do you notice thread migration issues?


On 21 Oct 2010, at 12:03 , Carsten Kutzner wrote:

> Hi,
> does anyone have experience with AMD's 12-core Magny-Cours
> processors? With 48 cores on a node it is essential that the processes
> are properly pinned to the cores for optimum performance.  Numactl
> can do this, but at the moment I do not get good performance with
> 4.5.1 and threads, which still seem to be migrating around.
> Carsten
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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