[Bioclusters] error while running mpiblast

[Aaron Darling]

Tim Cutts wrote:

>
> On 2 Mar 2005, at 5:59 am, James Cuff wrote:
>
>> mpiblast works.  Really very well for certain problems.  There I said 
>> it.
>>
>> Guy and Tim will probably never forgive me...  I think I may have 
>> been the
>> original 'embarrassingly parallel is the only way, nothing else will 
>> ever
>> give the throughput, yada, yada' advocate...
>
>
> Aargh - he's gone over to the Dark Side!!!
>
Haha!  You guys crack me up :-)   You will be assimilated.  Resistance 
is futile.

> Seriously, I agree with you.  MPIBlast gets you fast turnaround for 
> single very large searches.  I still think for the things Sanger are 
> doing we do better with the embarrassingly parallel model, but I 
> wouldn't claim that it's always the right solution (at least not any 
> more, he said, covering his tracks in case he's ever said exactly that 
> somewhere in the past)

For whatever it's worth, my opinion is that there are far better -- 
faster *and* more sensitive -- local alignment algorithms than BLAST and 
it's a shame they haven't come into wide use.  If (when) NCBI takes one 
of those better algorithms and calls it BLAST I bet it will get used.  
People know NCBI BLAST, people trust NCBI BLAST.  As long as that 
remains true there will be a place for parallel NCBI BLAST, and with 
huge databases even database segmentation will have a place.  What I 
really look forward to is for somebody to come up with a clever 
compression and searchable indexing scheme that accounts for the huge 
amount of redundancy in big databases like nt.  Then we won't need 
mpiBLAST anymore.

-Aaron