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

Doo Suk Yang microbe at CHOLLIAN.NET
Fri Mar 12 04:12:17 EST 1999

What about using SGI machine if affordable?
SGI announced parallelized version of BLAST for their machine.
I have no idea how fast it works but just saw its release note.
Check its home page

If you set it up, spread wide how fast it is.

On Thu, 11 Mar 1999, Andrew Martin wrote:

> 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.
> Andrew

Science is the game we play with God to find out what his rules are.
Doo Suk Yang                            Biotech Research Institute I
Research Scientist                      LG Chemical Ltd. Research Park
                                        104-1, Moonji-dong, Yusung-ku,
Voice: 82-42-866-2222                   Taejun, 305-390
FAX:   82-42-861-2566                   KOREA
A fool hath no delight in understanding, but that his heart may discover itself.
(Proverbs 18:2)

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net