[Beowulf] Lowered latency with multi-rail IB?

Mikhail Kuzminsky 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 
23:32:23 -0400):
>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.

Mikhail Kuzminsky
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.
>Best wishes,
>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
>336-334-5122 office
>336-334-4766 lab
>336-334-5402 fax
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