--U2hQUTaLKKEZj0t0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable ----- 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= h.edu) 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. Jon 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 > >Greetings > >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? > >Thanks. > >Cheers. > >Mike > >_______________________________________________ >Bioclusters maillist - Bioclusters@bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bioclusters > >----- End forwarded message ----- >=20 > >------------------------------------------------------------------------ > >_______________________________________________ >Beowulf mailing list, Beowulf@beowulf.org >To change your subscription (digest mode or unsubscribe) visit=20 >http://www.beowulf.org/mailman/listinfo/beowulf >=20 > ----- End forwarded message ----- --=20 Eugen* Leitl <a href=3D"http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --U2hQUTaLKKEZj0t0 Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux) iD8DBQFBiySmdbAkQ4sp9r4RAi6DAJ4poBOddXy0Um0Ua9gVC+62XnYPowCgin/B JICF2YSZT4l/dkc1fQfuVCw= =JmnT -----END PGP SIGNATURE----- --U2hQUTaLKKEZj0t0--