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
www.sgi.com/chembio
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
>>>
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