[Bioclusters] Direct connect infiniband/quadrics?

jason.calvert at novartis.com jason.calvert at novartis.com
Tue Mar 15 13:12:05 EST 2005

Depending on your applications, (Can you give us an Idea of which ones), 
you might want to look at a scalable multiprocessor system.  If you are 
not planning on expanding much, as it looks without a switch, you might 
get more bang for your buck with a 8 way box.  You can get an 8 way 
opteron box within your budget I would guess.  There would be some memory 
latency issues with more the 4 processors, but it will be faster than 
infiniband.  IBM offers some interesting hardware that might suit your 
needs.   The xSeries 445 scales from 4 processors up to 32 processors (8 
processors per 4u) and expands via an IBM interconnect giving you a large 
NUMA box.  I am not sure if they offer this with the nacona chipset so it 
might not work for you.  I fear we are way off the general topic of 
bioclusters now in any case :).

My 1/2 cnts.


Chris Dagdigian <dag at sonsorol.org>
Sent by: 
bioclusters-bounces+jason.calvert=pharma.novartis.com at bioinformatics.org
03/15/2005 12:42 PM
Please respond to "Clustering,  compute farming & distributed computing in 
life science informatics"

        To:     "Clustering,  compute farming & distributed computing in life science 
informatics" <bioclusters at bioinformatics.org>
        cc:     (bcc: Jason Calvert/PH/Novartis)
        Subject:        Re: [Bioclusters] Direct connect infiniband/quadrics?

It comes down to this:

There are very few applications in most areas of life science 
informatics that are (a) parallel aware enough to take advantage of a 
high-speed low latency interconnect like infiniband/quadrics and (b) 
actually written well enough to take advantage of the faster 
interconnect. There are some MPI codes out there that just use MPI for 
simple stuff  or API calls that do not actually run faster via the 
special interconnect layer.

So the usual case in bioclusters is "you don't need these sorts of 
interconnects at all because your science can't take advantage of them. 
They may be sexy to management types but generally its a waste of 

The exceptions are:

o people doing inhouse parallel development that desire to use these 
interconnects. These are typically smart people coding in Fortran or C++ 
and relatively few life sci inhouse software development groups have the 
skills to write true HPC codes.

o doing other "stuff" with the interconnect like clustering for HA or 
perhaps running a global/cluster filesystem over it

o people doing computational chemistry and molecular dynamics :)

You have personally found the big exception -- there are lots of 
commercial and non-commercial codes in the chemistry and molecular 
modeling spaces that actually are written for MPI and can (for most use 
cases) take advantage of the faster, lower-latency interconnects.

My $.02


Farul Mohd Ghazali wrote:
> Has anyone had any experience with a direct connect/point-to-point 
> implementation of Quadrics or Inifiniband? I talked to a small lab doing 

> some computational chemistry and molecular dynamics work and they're 
> interested in setting up a cluster but there is a need to justify the 
> cost of a cluster before the budget can be approved.
> During the discussion, the idea of using direct connect infiniband or 
> quadrics on two dual or quad Opteron nodes came up as a testbed platform 

> to justify to management. From a price point of view, this is very 
> attractive since it'll probably cost less than $40,000 (two quad 
> Opterons, two Quadrics cards) for a testbed system. Money is tight...
> So, is this setup workable? In theory this should be faster than a 
> gigabit based interconnect, even if it's just two nodes but I'd welcome 
> any other ideas/suggestions. Thanks.
> -- "Leadership & Life-long Learning" --
> Farul Mohd. Ghazali
> Manager, Systems & Bioinformatics
> Open Source Systems Sdn. Bhd.
> www.aldrich.com.my  Tel: +603-8656 0139/29   Fax: +603-8656 0132
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net
Bioclusters maillist  -  Bioclusters at bioinformatics.org

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