In message from Dow Hurst DPHURST <dphu...@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.
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 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
Moscow
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
__________________________________
Dow P. Hurst, Research Scientist
Department of Chemistry and Biochemistry
University of North Carolina at Greensboro
435 New Science Bldg.
Greensboro, NC 27402-6170
dphu...@uncg.edu
dow.hu...@mindspring.com
336-334-5122 office
336-334-4766 lab
336-334-5402 fax
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