suzen at theochem.tu-muenchen.de
Tue Jan 8 09:19:03 CET 2002
MyriNet may reduce communications overhead this is certain case. (Or
Dolphin) In my simulations
I gain around 30% over MyriNet. Since gromacs using
scaling should be fine. Also Kernel 2.4 gives better TCP performace,
which should be take into
Justin MacCallum wrote:
> I have a couple of questions/comments regarding scaling over gigabit
> Our hardware vendor has given us three gigabit ethernet (Intel PRO/1000T
> Server) and a switch (Intel NetStructure 470T) for evaluation. We have
> dual PIII 1Ghz nodes in our cluster. I tried two test systems. The first
> one was a 64 lipid DOPC bilayer with ~11000 atoms. The second was a box
> of water containing 81000 atoms. Both systems used a 0.9 rlist, 1.4 rdw
> and 0.9 rcoulomb with PME, order=4, fourierspacing=0.12, optimize_fft=yes.
> For both systems I ran two simulations, one on two processors and one on
> four. For both systems, the two processor version performed slightly
> better than the four processor one. In both cases, the network load in
> the four processor versions was about 5%. Based on previous benchmarks on
> fast ethernet nodes, I expect things to scale much better without PME.
> >From this I've concluded that for our hardware and systems we are latency
> bound. In order to improve scaling we need to move to an interconnect
> with lower latency, such as myrinet, or stop using PME. Does this sound
> right? Also, does anyone know of any kernel parameters that may be
> tweaked to improve latency on gibabit or fast ethernet?
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