Local BLAST server - any experience on dual/quad Intel - Linux platforms

Andrew Martin amartin at stagleys.demon.co.uk
Thu Mar 11 05:41:39 EST 1999

Harry Mangalam (mangalam at uci.edu) wrote:
: I'm considering using a dual Pentium II/Celeron, unless I can get
: feedback that BLAST does not work well on such a system, in which case
: we would run either a uni-PII/Celeron or if more $ can be scraped up, an
: Alpha (but having experience with Linux/Alpha, I know some of the
: problems with that approach).

Don't bother with Alpha for BLAST - price/performance is not up to it.
A 533MHz Alpha box costs about 50% more than an Intel PentiumII-400 and 
gives a 20% speed increase for BLAST. Alpha shines where there is lots of
floating point. There also seem to be some problems in the maths 
libraries with over/underflow causing BLAST to core dump or stop if
the E-value is extremely significant (e.g. when a sequence hits
itself). Compaq have now released their Digital Unix maths libraries
for Linux, so this problem may be solved by using those.

I can't really comment on using an SMP machine, but my impression is
that only parts of BLAST are threaded, so you will get far from a 2x
speedup - probably a good option if you want to run 2 BLASTs at once
though since you don't have the overhead of disks etc. (providing you
have enough memory to fit the DB in memory twice).

We've also done some tests on different disks under Linux and don't
see any significant speedup by going from UDMA to UW-SCSI or U2W-SCSI.


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