[Bioclusters] cluster hardware question

Duzlevski, Ognen bioclusters@bioinformatics.org
Thu, 16 Jan 2003 08:13:34 -0600 (CST)

Hi Joe,

thanks for sharing your knowledge with me.

> Often overlooked in clusters until too late is Disk and IO in general.
> Chris Dagdigian at BioTeam.net is a good person to speak to about this.

When you say "Disk and IO", do you mean storage over fiber, local node
hard-drives...? What would be good choices for your typical bioinformatics
shop - I have seen options between local nodes having the latest SCSI
drives and nodes having the regular 5400 rpm ide drives. Does it pay to go
with compute node SCSI 10000 rpm or is a 7200 rpm ide good enough?

> > Also very much overlooked is the issue of cluster management.  This
> tends to guide the choice of Linux distribution.  Management gets to be
> painful after the 8th compute node, the old models don't work well on
> multiple system image machines.

What are the usual choices here? Any recommendations, web-sites, companies
I should be looking at in particular? 40 nodes would be our starting point
but we could easily move up to more in time. Many vendors offer various
alternatives - I think personally I would like to have something that is
easy to understand and is not a complete black box.

> There are other issues as well, specifically networking, backup of
> system, extra IO capabilities, etc.

Joe, I know this could easily turn into a thick book :), but how does one
get more educated about these things?

Another question that I am curious about is Itanium 2 and using them in a
cluster - any experiences with these? How about bioinformatics software -
any benefits in your regular programs like blast, clustalw... when running
on an itanium system?

Thank you,