[gmx-developers] gromacs @ AMD Interlagos

[David van der Spoel]

On 2012-05-01 10:44, Carsten Kutzner wrote:
> 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 :)
>
Would be great if you could try it.

If it is the case that two core share one FPU/SSE unit than we have two 
threads competing for the FPU/SSE unit and that would definitely slow 
things down. On the other hand having double the amount of threads 
should give some speed up in other parts such as neighbor searching, 
such that the final result with 24or 48 threads should be comparable. It 
seems that this is not the best architecture for FP intensive codes if 
all this holds.

-- 
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