[Bioclusters] mpiBLAST Performance

[Osborne, John]

>Each node will get one piece. If you fragment the database using the
command
>mpiblast -N 20 ...

I thought fragmenting was done only by mpiformatdb?

When do I want to use the -N option and not -np (as in the README file)?

>you will get 21 fragments. When you run mpiblast, however, you should
provide 22 machines
>(21 workers + 1 master). If you specify less than 22 nodes, at least one
>node will have to process more than one fragment (with the associated cost
of 
>of copying the needed database fragment and the accumulation of multiple 
>database fragments on multiple nodes).
>
I'm not sure how you provide the master node exactly, I have just included
mine
making it node 0.  Why do you provide 22 machines for 21 fragments?

>Also, while not a factor when blasting against the nr database, shuffling
the 
>nt database yields a substantial speed increase in blast searches (I have
obtained
>a 28% decrease in wall clock time for certain nucleotide queries).
>
Shuffling?

 -John