From: Norman Geist (
Date: Mon May 12 2014 - 01:12:54 CDT

Regarding your original problem, are you using smp or fully mpi/charm++?

> -----Ursprüngliche Nachricht-----
> Von: [] 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
> <> 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

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