http://www.penguincomputing.com/cluster_computing
Can the above be of any help to you ? Regards Prajeev On Fri, Mar 27, 2009 at 11:16 AM, Dow Hurst DPHURST <[email protected]>wrote: > To: [email protected] > From: Greg Lindahl <[email protected]> > Sent by: [email protected] > Date: 03/27/2009 12:03AM > Subject: Re: [Beowulf] Lowered latency with multi-rail IB? > > 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. > > BTW, Intel MPI usually has higher latency than other MPI > implementations. > > If you look around for benchmarks you'll find that QLogic InfiniPath > does quite well on NAMD and friends, compared to that other brand of > InfiniBand adaptor. For example, at > > http://www.ks.uiuc.edu/Research/namd/performance.html > > the lowest line == best performance is InfiniPath. Those results > aren't the most recent, but I'd bet that the current generation of > adaptors has the same situation. > > -- Greg > (yeah, I used to work for QLogic.) > > _______________________________________________ > Beowulf mailing list, [email protected] > To change your subscription (digest mode or unsubscribe) visit > http://www.beowulf.org/mailman/listinfo/beowulf > > > I'm very familiar with that benchmark page. ;-) > > One motivation for designing a MPI layer to lower latency with multi-rail > is when making use of accelerator cards or GPUs. There is so much more work > being done that the interconnect quickly becomes the limiting factor. One > Tesla GPU is equal to 12 cores for the current implementation of NAMD/CUDA > so the scaling efficiency really suffers. I'd like to see how someone could > scale efficiently beyond 16 IB connections with only two GPUs per IB > connection when running NAMD/CUDA. > > Some codes are sped up far beyond 12x and reach 100x such as VMD's cionize > utility. I don't think that particular code requires parallelization (not > sure). However, as NAMD/CUDA is tuned, the efficiency on the GPU is > increased, and new bottlenecks found and fixed from previously ignored > sections of code, there will be even more than a 12x speedup. So, a > solution to the interconnect bottleneck needs to be developed and I wondered > if multi-rail would be the answer. Thanks so much for your thoughts! > Best wishes, > Dow > > _______________________________________________ > Beowulf mailing list, [email protected] > To change your subscription (digest mode or unsubscribe) visit > http://www.beowulf.org/mailman/listinfo/beowulf > >
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