[Beowulf] [landman at scalableinformatics.com: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)]

Eugen Leitl eugen at leitl.org
Fri Jan 13 11:15:12 PST 2006

----- Forwarded message from Joe Landman <landman at scalableinformatics.com> -----

From: Joe Landman <landman at scalableinformatics.com>
Date: Fri, 13 Jan 2006 13:59:25 -0500
To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>
Subject: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)
X-Mailer: Open WebMail 2.51 20050615
Reply-To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>

Hi Farul:

On Fri, 13 Jan 2006 22:46:04 +0800, Farul Mohd. Ghazali wrote
> Some years back when Timelogic and Paracel were popular there were
> some discussions on FPGA based computing for Linux clusters. I can't
> recall if there was a general conclusion but one of the limitations
> was that you're stuck with the algorithms the manufacturer provided.

  In some cases this is true (TimeLogic, et al: Paracel went under).  The
reality of today is quite different for board based units.  There you can use
any number of technologies to map your algorithm to the card.

> SGI approached me recently to talk about their reconfigurable FPGA
> systems and I was intrigued. The new RASC allows a user to remap the
> FPGA according to your own algorithms instead of being limited to one
> set of libraries. They also link it with GNU tools for debugging etc.

This isn't restricted to SGI.  There are folks selling C to VHDL/Verilog
compilers out there.  You will not get as good performance as hand designing
the circuit, but it is certainly a start.

Think of it like the old autoparallelizers. They didn't give you linear
speedups.  What they did is give you "good enough" in many cases, or got you
started on your way to accelerate more.

> Has anyone looked at the SGI RASC or any other equivalent system out
> there? Any ideas if it makes sense in today's clusters? The workload

<bias alert>

I would avoid things that look proprietary to vendors whom are not doing so
well in the market.  Unless the thing is open and available from others when
and if SGI goes away, that is a good enough reason to look at similar
technology from open vendors.

We work with a company that designs and builds such cards and software.  If
you are interested, we can get you more info.  This would be for offline so as
not to spam everyone.


> I'm supporting has very few custom written algorithms and is mostly
> BLAST, phred/phrap, hmmer with some heavy Amber and Gromacs thrown in
> as well.

Today, accelerating integer apps (SW, HMMer, MSA) isn't too painful on
"commodity" accelerator cards (available over the counter).  The cards plus
software will run into a little money (about 2-4 compute nodes worth), but
give you stellar performance (10-100 compute nodes worth).  Accelerating
floating point intensive applications cannot easily be done today on FPGA's,
as FPGA's don't have enough gates for lots of IEEE754/854 units.  This will
change over time, but it will take a while.  If you can live with non-IEEE
math (you need to think over the implications of this very carefully), you
have many options, some of which are terribly interesting.

That said, some very interesting things are on the horizon that should address
Amber and Gromacs among other dynamics codes.


> TIA.
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

Scalable Informatics LLC
phone: +1 734 786 8423

Bioclusters maillist  -  Bioclusters at bioinformatics.org

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Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
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