[Beowulf] [Bioclusters] Cluster specs (fwd from muratem@eng.uah.edu) (fwd from jonbernard@uab.edu)

Eugen Leitl bioclusters@bioinformatics.org
Fri, 5 Nov 2004 07:58:46 +0100

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----- Forwarded message from Jon Bernard <jonbernard@uab.edu> -----

From: Jon Bernard <jonbernard@uab.edu>
Date: Thu, 04 Nov 2004 16:37:26 -0600
To: Eugen Leitl <eugen@leitl.org>
Subject: Re: [Beowulf] [Bioclusters] Cluster specs (fwd from muratem@eng.ua=
User-Agent: Mozilla Thunderbird 0.8 (Windows/20040913)

The standard cheap solution these days seems to be dual Opterons with=20
2GB of RAM, connected via GigE, running one of the free offshoots of=20
RedHat. If you have only a few applications, you optimize for those --=20
whether faster CPUs, more RAM, or faster interconnects -- assuming=20
non-technical issues don't force your hand. Blades are typically more=20
expensive upfront, but use less space and power, so they may save you=20
money in the long run.

Our cluster, though in a mechanical engineering dept, is used about 1/2=20
to 2/3 of the time for bio applications. Some of those applications are=20
embarrasingly parallel; others are highly dependent on the network. The=20
only difference between our engineering codes and the ones used by bio=20
researchers is that usually we don't have source for the bio stuff, and=20
binaries are usually available only for i386 Linux. Other than that I=20
can't, myself, see how a bio-cluster differs from an engineering cluster.


Eugen Leitl wrote:

>----- Forwarded message from Mike Muratet <muratem@eng.uah.edu> -----
>From: Mike Muratet <muratem@eng.uah.edu>
>Date: Thu, 4 Nov 2004 12:01:38 -0600 (CST)
>To: bioclusters@bioinformatics.org
>Subject: [Bioclusters] Cluster specs
>Reply-To: bioclusters@bioinformatics.org
>The local university is preparing a proposal for a cluster and has asked
>for inputs. As is often the case, by the time the request trickles down to
>those who actually have to provide the informaton, the response is due.
>So, if I could impose upon the experience of those on the list, I need to
>refresh my knowledge about clusters and figure out what the state of the
>art is these days. I feel like one of those guys that is trying to get
>their CS homework done on the perl list, but here goes...
>* Platform: I like Red Hat or SUSE linux on Athlons (preferable to me) or
>Pentiums. I've done a lot of teeth-grinding trying to get things to run on
>Macs. But, I think there may be compelling performance arguments for
>Apple. Could anyone make such an argument? Anybody have any comments about
>Blade technologies?
>* Cluster system: the biocluster webpage talks about approaches for
>bioclusters being "...significantly different from
>traditional HPC and "beowulf-style" approaches" and I certainly buy into
>this. Has anybody thought any about _why_ it's different and would
>they like to share it? I've used Sun GridEngine. Has anybody come up
>with anything that has more synergy? Is there any open source BLAST out
>there that exploits the cluster environment?
>Bioclusters maillist  -  Bioclusters@bioinformatics.org
>----- End forwarded message -----
>Beowulf mailing list, Beowulf@beowulf.org
>To change your subscription (digest mode or unsubscribe) visit=20

----- End forwarded message -----
Eugen* Leitl <a href=3D"http://leitl.org">leitl</a>
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