[Bioclusters] Call for information.

Paul Gardner bioclusters@bioinformatics.org
Wed, 17 Apr 2002 12:52:56 +1200 (NZST)

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.


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
>William Park, Open Geometry Consulting, <opengeometry@yahoo.ca>
>8 CPU cluster, NAS, (Slackware) Linux, Python, LaTeX, Vim, Mutt, Tin
>Bioclusters maillist  -  Bioclusters@bioinformatics.org