Performance of Linux systems for BLAST searching??

Andrew Martin amartin at stagleys.demon.co.uk
Sun Dec 6 19:08:42 EST 1998

Dave Kristofferson (kristoff at NET.BIO.NET) wrote:

: I'm thinking about setting up an in-house BLAST server on a limited
: budget and was wondering what kind of performance people are getting
: out of Linux machines these days.  I've received some attractive
: quotes on 600 MHz Alpha and dual 450 MHz Pentium II systems with 1 GB
: of RAM in the $6,000 - $8,000 range.  I'd be interested in hearing
: people's experiences with similar systems.

: Sincerely,

: Dave Kristofferson

Alpha works great if you compile using DEC CC under Digital Unix then use the
executable. Not so good complied with GCC under Linux. About 30% slower
for a start. Also there seem to be some probs. with the maths libraries
and PSI-BLAST as opposed to BLAST crashes randomly. (BLAST also crashes,
but there is a fairly straightforward fix (one of the maths calls
causes a numeric underflow in calculating E from the bit-score).

Hope that helps,


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