[Bioclusters] error while running mpiblast

Tim Cutts tjrc at sanger.ac.uk
Thu Mar 3 17:41:57 EST 2005

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!!!

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)

>> Note: We have not built the mpiblast RPM for Itanium (nor for that
>> matter, any of our RPMs).  Is there any interest in this?  Curious.
> Shame they cost so darn much, well ours do, but folk keep demanding me 
> to
> cram 64GB in them for something called whole genome assembly.  I just
> can't for the life of me understand why they cost so much :-)

It's a good argument for getting people to write more memory-efficient 

"And just how many times your annual salary does the memory you're 
asking for cost?"


Dr Tim Cutts
Informatics Systems Group, Wellcome Trust Sanger Institute
GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233

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