[gmx-developers] gromacs @ AMD Interlagos

[Carsten Kutzner]

On May 1, 2012, at 10:26 AM, David van der Spoel wrote:

> On 2012-05-01 09:19, David van der Spoel wrote:
>> Hi,
>> 
>> we have done some very preliminary benchmarks on AMD Interlagos nodes, 4
>> CPUs with 12 cores each. After hearing a report that in fact on these
>> machines 2 cores share an FPU and a SSE unit, a colleague tested a
>> simple protein in water:
>> 
>> ... after a short 1 ns test run, the 24 (2x12) core solution
>> outperformed the 48 core one (16.3 ns/day vs. 1.4 ns/day). Restraint on
>> protein heavy atoms, NVT, waters mobile, ca. 38000 atoms.
>> 
>> Can anyone confirm this result? It seems excessive to me.
>> 
> What this would imply, if confirmed, is that we would need to allocate only half the number of threads on this architecture, compared to the number of cores.
Hi David,

we get a performance on our Interlagos nodes that is comparable to
the Magny-Cours. I would guess there is something wrong in 
your case. Is the kernel recent enough?
For a 80,000 atom test system with PME, we get about 15 ns/day both
on 48 Magny-Cours cores as well as on 48 Interlagos cores.
I have not tries with 24 Interlagos cores yet, but maybe it's
faster :)

Best regards,
   Carsten
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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