[Beowulf] latency vs bandwidth for NAMD

Dow Hurst DPHURST DPHURST at uncg.edu
Wed Aug 22 12:52:30 EDT 2007


Jim and Kevin,
Why would the 4 core point on the performance benchmark be reversed between
the 2.66GHz and 3.0GHz?  I'm pretty sure that the Lonestar NAMD was
compiled with the Intel compilers.  I don't know what was used on the
Cambridge Darwin cluster.  Both machines are Intel Woodcrest dual cores and
dual physical CPUs per node.

Both Infinipath clusters listed on the performance benchmark have the best
scaling for the apoa1 benchmark between 128 to 512 cores.

Sure seems if SDR is good enough for an Intel Clovertown based cluster that
that would be more cost effective.  The Woodcrest and Clovertown are priced
about the same.

Thanks for your comments!
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
dphurst at uncg.edu
Dow.Hurst at mindspring.com
336-334-4766 lab
336-334-5122 office
336-334-5402 fax

-----Jim Phillips <jim at ks.uiuc.edu> wrote: -----

To: Kevin Ball <kevin.ball at qlogic.com>
From: Jim Phillips <jim at ks.uiuc.edu>
Date: 08/22/2007 12:25PM
cc: Dow Hurst DPHURST <DPHURST at uncg.edu>, beowulf at beowulf.org
Subject: Re: [Beowulf] latency vs bandwidth for NAMD


Those NAMD results are up now ("Cambridge Xeon/3.0 InfiniPath" at
http://www.ks.uiuc.edu/Research/namd/performance.html).  My opinion is
that SDR is sufficient for NAMD, but I haven't had a chance to see if
there is any benefit to DDR.  I did hear that the new TACC Ranger cluster
with 16 cores per node will use SDR.  I assume that on larger clusters the
switch is more likely to be the limiting factor than the card (I know
precious little about either).

-Jim


On Tue, 21 Aug 2007, Kevin Ball wrote:

> Hi Dow,
>
>  The QLE7240 DDR HCA is not available yet, but we do not expect that it
> would have any substantial advantage on NAMD as compared to the QLE7140
> (SDR), because we don't believe that NAMD requires substantial pt to pt
> bandwidth from the interconnect.
>
>  The TACC cluster is not using QLogic InfiniBand (IB) cards, but I
> believe they are SDR IB cards from another vendor.
>
>  Just last week I submitted a result to the folks at UIUC with results
> on a similar cluster with the QLE7140.  It has not yet shown up on their
> results page, but in essence, the scalability is similar until around
> 256 cores, at which point the results diverge with the QLE7140 cluster
> dramatically outperforming the TACC cluster at 512 cores.
>
>  I expect the QLE7140 results will show up in the next week or so on
> that website, (http://www.ks.uiuc.edu/Research/namd/performance.html) so
> you can compare to TACC performance at that time.  On that site you can
> also see performance with a number of other machines, including an SGI
> Altix with much higher pt to pt bandwidth yet worse scaling than IB,
> which is part of why I don't think DDR will improve results.
>
>  If you are interested in other MD codes, we have found advantages on
> codes like CHARMM and GROMACS as well.  Some of thsee are detailed in a
> white paper on our website:
>
http://www.qlogic.com/documents/datasheets/knowledge_data/whitepapers/HSG-WP07005.pdf

>
>  Fair notice:  I work for QLogic on the InfiniPath product line.  I
> have tried my best to make what bias I have open and clear.
>
> -Kevin
>
>
> On Fri, 2007-08-17 at 14:03, Dow Hurst DPHURST wrote:
>> I'd like to get advice on how latency affects scaling of molecular
dynamics
>> codes versus total bandwidth of the interconnect card.  We use NAMD as
the
>> molecular dynamics code and have had Ammasso RDMA interconnects.  Right
>> now, we have a chance to upgrade and add nodes to our cluster using
>> Infiniband.  I've found that NAMD was coded to be latency tolerant,
>> however, I'd like to scale up to 64 cores and beyond.  I'm going blind
>> reading IB card specs, performance benchmarks, and searching Google.
I'd
>> love some advice from someone who knows whether a consistent very low
>> latency IB card, such as the Infinipath QLE7140, is better/worse for
NAMD
>> than a higher latency but higher bandwidth card such as the QLE7240?  I
can
>> tell that Lonestar at TACC has great NAMD performance but I can't tell
what
>> IB card is used.  I imagine that switch performance plays a large role
too.
>> Thanks for your time,
>> Dow
>>
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