[Bioclusters] Direct connect infiniband/quadrics?

Chris Dagdigian dag at sonsorol.org
Tue Mar 15 12:42:39 EST 2005

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 money...".

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
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