[Beowulf] Lowered latency with multi-rail IB?
kus at free.net
Fri Mar 27 10:58:20 PDT 2009
In message from Dow Hurst DPHURST <DPHURST at uncg.edu> (Thu, 26 Mar 2009
>We've got a couple of weeks max to finalize spec'ing a new cluster.
>anyone knowledge of lowering latency for NAMD by implementing a
>multi-rail IB solution using MVAPICH or Intel's MPI? My research
>me low latency is key to scaling our code of choice, NAMD,
>effectively. Has anyone cut down real effective latency
>to below 1.0us using multi-rail IB for molecular dynamics codes such
>Gromacs, Amber, CHARMM, or NAMD? What about lowered latency for
>parallel abnitio calculations involving NwChem, Jaguar, or Gaussian
>using multi-rail IB?
In opposition to molecular dynamics programs (Gromacs/Amber/Charmm)
where low latency is necessary, for some quantum chemical programs
(Gaussian, Gamess-US) there is relative low interconnect dependency.
I measured message lengthes for Gaussian-03 for a set of calculation
methods, and this messages are middle-to-large in sizes. NWChem is the
only quantum-chemical program I know, which require high interconnect
performance. I don't know about Jaguar.
Computer Assistance to Chemical Research Center
Zelinsky Institute of Organic Chemistry RAS
>If so, what was the configuration of cards and software? Any caveats
>involved, except price?
>Multi-rail IB is not something I know much about so am trying to get
>up to speed on what is possible and what is not. I do understand
>that lowering latency using multi-rail has to come from the MPI layer
>knowing how to use the hardware properly and some MPI implementations
>have such options and others don't. I understand that MVAPICH has
>some capabilities to use multi-rail and that NAMD is run on top of
>MVAPICH on many IB based clusters. Any links or pointers to how I
>can quickly educate myself on the topic would be appreciated.
>Dow P. Hurst, Research Scientist
>Department of Chemistry and Biochemistry
>University of North Carolina at Greensboro
>435 New Science Bldg.
>Greensboro, NC 27402-6170
>dphurst at uncg.edu
>Dow.Hurst at mindspring.com
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