On Mar 27, 2009, at 6:20 , Nifty Tom Mitchell wrote:
On Thu, Mar 26, 2009 at 09:03:30PM -0700, Greg Lindahl wrote:
On Thu, Mar 26, 2009 at 11:32:23PM -0400, Dow Hurst DPHURST 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?
Multi-rail is likely to increase latency.
In genetral true, but it depends. With a heavy all-to-all
communication pattern, I have seen intelligent use of two HCAs (not
muiltirail per se in order to increase bandwidth). I have observed
almost 2x performance increase on SPEC MPI2007 pop2 application when
going from one to two HCAs. This is a typical many-small-packets
application.
I am not saying the same is true for NAMD, but I wouldn't rule it out.
BTW, Intel MPI usually has higher latency than other MPI
implementations.
Intel MPI and MVAPICH is not what I would call top-of-the-line
performers (but I am biased as I work for a company delivering an MPI
product). You might find it useful to look at pop2 performance for
different interconnects and MPI implementations at ttp://www.spec.org/mpi2007/results/mpi2007.html
Thanks, Håkon
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