[Bioclusters] Call for information.

Goran Ceric bioclusters@bioinformatics.org
Wed, 17 Apr 2002 00:05:54 -0500 (CDT)

Let me interfere for a second. Real parallel applications (those using MPI, 
PVM etc.) are cool and they can definitely impress people, especially those 
people who write checks. The real power of Linux clusters, however, lies in 
their ability to run a huge number of serial jobs. There are several 
reasons why I'm saying this. First, most bioinformatics applications are 
not parallelized (again, using MPI, PVM etc.), and second if you want to 
use real parallel applications, you can't do that over fast Ethernet. I 
mean, you certainly can, but you'd take a huge performance hit. In order to 
maximize the efficiency, you'd have to invest in Myrinet or something 
similar and networking would cost you more than your cluster. 

For $256K, you can get yourself ~128-cpu (64 dual PIII, 1U) cluster + 
networking + rack + everything else, but don't buy it if you're not going 
to use it often. We've got 128-cpu (PIII,1GHz,PBSPro/Maui, yada yada) 
cluster here and the reason why we went with Intel and not AMD was that (at 
that time) there wasn't a company I could trust and rely on (hardware 
support) that sold SMP Athlon systems. Also, have in mind that most of the 
stuff you'd run is integer and not FP intensive. That's my $0.02.

Goran Ceric
System Administrator
Washington University St. Louis
Department of Genetics, Eddy Lab


> Hi All,
> Well thanks for your replies (Ivo, Josh, William). Unfortunately I
> think we've got off the topic a bit. Obviously the Pentium vs Athlon
> debate is a popular discussion.  The only reason we're not considering
> the Athlon solution is that our University has a ridiculous contract
> with a Hardware provider that doesn't supply Athlon chips.
> What I'm really interested in is what applications are others using
> BioClusters for. Such as parallel implementations of BLAST, hmmsearch,
> protein folding, etc. I want my Biologist colleagues to know the
> amazing capabilities and benefits they will recieve from using a
> cluster.
> Also, thanks a lot for your email Chris. What sort of experiments were
> your pharma company able to implement with the aid of your blast farm?
> And what are these urls you promised? ;-)
> I personally use our cluster to fold lots of RNA sequences (using
> Vienna) with an embarassingly parallel implementation. I love the fact
> that my simulations that would normally take months to complete are
> finished in just a few days.
> Cheers,
> Paul.
> On Tue, 16 Apr 2002, William Park wrote:
>>On Wed, Apr 17, 2002 at 02:13:14AM +1200, Paul Gardner wrote:
>>> Hi William,
>>> I already have several problems that I could extend beyond our
>>> current computing solution (16 node Beowulf: sisters.massey.ac.nz).
>>> The problem is convincing a few senior scientists (hope that answers
>>> your question Chris, thanks heaps) who've recently received a large
>>> government grant that spending a bit of money upgrading our current
>>> system is worth while. Basically I want my Biologists friends to know
>>> that they'll also benefit from the power of a cluster.
>>> I agree that Athlons are probably a better way to go, but
>>> frustratingly there are some other issues that have made us consider
>>> PentiumIVs as a better solution.
>>Well, what do they want?  More nodes for current clusters, or new
>>computers on their desks?
>>Cluster is not all that's cracked up to be.  After spending all that
>>money building dual-P3 cluster a year ago, I'm a bit pissed to find
>>that current 1 dual-MP will practically replace it.  Your situation is
>>probably the same.
>>William Park, Open Geometry Consulting, <opengeometry@yahoo.ca>
>>8 CPU cluster, NAS, (Slackware) Linux, Python, LaTeX, Vim, Mutt, Tin
>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bioclusters