Diskless for Bioinformatics?
wrp at virginia.edu
Fri Jun 22 13:17:49 PDT 2001
> Message: 2
> From: Brian LaMere <blamere at diversa.com>
> To: "Beowulf List (E-mail)" <beowulf at beowulf.org>
> Subject: diskless clients? beowulf-newbie seeks advice
> Date: Fri, 22 Jun 2001 10:55:08 -0700
> why does every guide around talk about diskless clients? I
> mean...disks are
> stinkin cheap nowadays...
> I have ~$150,000 to make a test cluster (with WAY more if the test
> shows worth) but the boss-man wants to go with nodes which aren't
> "commodity" in my book. dual p3-1000 with 1.25Gb ram, 15krpm 18Gb
> The things cost $8k+ each...tried to explain that 148 $1k machines
> would way
> out perform 16 $8k machines, but...oh well. These boxes take up 1u,
> seems to be their main selling point (HP's lp1000r). Fortunately, these
> boxes are down to $6.5k now in cost (dropped a bit since we bought
> them a
> couple months back), but still...
There is a lot to be said for dual processor machines for Bioinformatics
Many of the applications, like HMMER, FASTA, and perhaps BLAST, run out
so you really get 2X speedup on 2 CPU's. We purchased SuperMicro 1U
dual PIII machines
with 18 Gb SCSI (10K), 512 Mb RAM for about $3K each about 4 months ago.
> Just a little genetics research firm, needing some serious horsepower to
> start running big hammer and blast jobs. The data we have now is just
> bare minimum we need to get by, but if we had things like a working
> the scientists upstairs would start making, since they'd be able to use
> much more data.
I think you want disks - they make it easier to debug a node separately,
and for your BLAST applications (which will not run in parallel, you
must run many separate instances) you can have all 16-32-64 CPU's
loading up the database independently.
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