[Bioclusters] Request for discussions-How to build a biocluster Part 6 (Misc.)

Jim Kent bioclusters@bioinformatics.org
Thu, 02 May 2002 16:09:18 -0700

We use BLAT mostly - it's much much faster than BLAST, and
can cope with introns.   You can run multiple programs on a
cluster.  The job scheduler - LSF, SGE, PBS, Parasol or whatever
gives the jobs to the machines one at a time typically.

Jim Kent  
Genome Bioinformatics Group
University of California at Santa Cruz

----- Original Message ----- 
From: "Sylvain Foisy" <foisys@mac.com>
To: <bioclusters@bioinformatics.org>
Sent: Thursday, May 02, 2002 10:57 AM
Subject: [Bioclusters] Request for discussions-How to build a biocluster Part 6 (Misc.)

> Hi,
> A reminder: this is coming from a total newbie at this BioCluster stuff. 
> it is also to serve as the seed of a tutorial/history-of-building site 
> for our creation. I am a total newbie in UNIX administration and 
> installation. This is why we will get a system administrator to help us 
> out. But I still have to figure out the right questions to ask!!
> Besides BLAST, what other bioinfo software are known to work in cluster 
> config? I would imagine that FASTA, the HMMER suite and any software 
> that work in embarrassingly parallel fashion will. Anybody has 
> experience running multi-softwarer clusters?
> Also, can a cluster do let's say, BLAST and RNA folding together? or 
> BLAST and molecular modelling? At 8 nodes, we will concentrate on BLAST 
> but we are planning a 32 nodes stage soon afterward and the demand is 
> there.
> Another point that has been raised in our group is the fact that if some 
> clusters might be less busy than others, is it possible for the head of 
> the busy one to get help from the nodes of a less busy cluster? I ask 
> because our projected cluster is to be a public-access resource. Another 
> cluster is also planned for philogeny analysis by a group in the same 
> department. In exchange for maintaining a mirror of GenBank, they are 
> offering some of their horsepower to us. Is this feasible?
> Am I missing something?
> This is open for helpful and constructive discussion
> I know that lots of my questions have been asked before but I found some 
> of the answers to be very cryptic. By pooling my questions in this 
> multipost, I invite discussion on the hows of putting a BioCluster 
> together for the less technically inclined among us!
> Sylvain
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Sylvain Foisy, Ph. D.
> Manager
> BIONEQ - Le Reseau quebecois de bioinformatique
> Genome-Quebec
> Tel.: (514) 343-6111 poste 5188
> E-mail: foisys@medcn.umontreal.ca
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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