From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 27 2009 - 09:28:40 CDT
On Fri, Mar 27, 2009 at 1:05 AM, Dow Hurst <Dow.Hurst_at_mindspring.com> wrote:
> Just found this link which doesn't make sense to me as latency seems more
> important than bandwidth for NAMD.
> Any thoughts?
thanks to using the charm++ and the fact that the real space non-bonded and
the k-space coulomb contributions can be computed independently, NAMD can
do a significant amount of latency hiding. if you want to build a high
machine (many jobs but each run somewhat slowish) then you can even get
away with tcp/ip and gigE. in the limit of scaling you'll first notice
overhead of MPI (as charm++ has to do a lot of polling), this can be avoided
but compiling charm++ to run on the infiniband layer directly which
primitives that are much more suitable for charm++ than for MPI.
not sure what state that part of charm++ is currently in, though. last
time i tried
(quite a while back), it didn't work reliably on our local hardware.
i'd thus ask
the charm++ folks for help on this subject.
latency _is_ an issue for _other_ MD codes that cannot hide them.
> Best wishes,
> Dow Hurst wrote:
>> We've got a couple of weeks max to finalize spec'ing a new cluster. Has
>> anyone knowledge of lowering latency for NAMD by implementing a multi-rail
>> IB solution using MVAPICH or Intel's MPI? My research tells me latency is
>> key to scaling effectively. Has anyone cut down latency to below 1.0us
>> using multi-rail IB?
>> If so, what was the configuration of cards and software? Any caveats
>> Anyone run NAMD on top of Appro's enhanced version of Intel's MPI in a
>> multi-rail configuration?
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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