From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon May 12 2014 - 12:06:53 CDT
Me, SMP on a system of ~83'000 atoms (which is somewhat representative of
what we currently use NAMD for here).
Robert and Joseph, I don't know.
On 05/12/2014 02:12 AM, Norman Geist wrote:
> Regarding your original problem, are you using smp or fully mpi/charm++?
>
>> -----Ursprüngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Brunner, Robert Kraemer
>> Gesendet: Freitag, 9. Mai 2014 19:04
>> An: Namd Mailing List
>> Betreff: Re: namd-l: NAMD and NUMA
>>
>>
>> On May 9, 2014, at 11:45 AM, Kenno Vanommeslaeghe
>> <kvanomme_at_rx.umaryland.edu> wrote:
>>
>>> I'm not convinced this is true. The shared FPU on an AMD bulldozer
>> module is 256 bits wide and a single thread can only saturate it
>> through relatively intensive use of AVX instructions. Given more real-
>> life like workloads, it acts as two 128-bit FPUs. Last time we
>> benchmarked, we could actually make NAMD run substantially faster by
>> using all the logical cores, though the speedup was significantly lower
>> than the one we saw when comparing the same numbers of cores on a
>> machine with twice as many modules (frequency scaling might also play a
>> role there). The same could not be said of our Intel benchmarks, where
>> the speedup from using all the virtual cores was nearly negligible. For
>> fairness, it should be noted that Intel *also* has these wide FPUs (and
>> wider in more recent iterations) that are shared between threads, so we
>> ascribed the difference to more aggressive frequency scaling from
>> Intel's part.
>>
>>
>> Our experience with NAMD on Blue Waters (which uses Bulldozer
>> processors) is that using all the logical cores is usually slightly
>> faster than only 1 thread per FP unit, but the difference is not huge.
>> Problem size is undoubtedly a factor; at some point communication
>> starts to dominate and the difference in FP performance doesn't matter.
>>
>> Robert
>>
>>
>>
>>
>> ----------------------------------------------
>> Robert Brunner
>> Blue Waters Science and Engineering Applications Support
>> National Center for Supercomputing Applications
>> 4006F NCSA Building, MC-257
>> 1205 W Clark St
>> Urbana, IL 61801
>> 217-333-7677
>> rbrunner_at_illinois.edu
>>
>>
>>
>
>
>
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