[Beowulf] latency vs bandwidth for NAMD

Jim Phillips jim at ks.uiuc.edu
Wed Aug 22 12:25:57 EDT 2007


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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