Heshan Lin's publication "Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture" at SC|08 demonstrated that mpiBLAST 1.6.0 can scale across 32,768 compute cores with 93% efficiency on an IBM Blue Gene/P.
Previously, Aaron Darling's presentation at BOSC 2005 details the performance evolution of mpiBLAST from v0.9 to v1.4.0. In short, mpiBLAST v1.4.0 has a 305x speedup on 128 workers and decreases the search time for E. chrysanthemi (300KB) against the NT database (14GB unformatted) from 2 days to 10 minutes on Green Destiny.
Also, we are looking for test cases from users to help us profile and improve mpiBLAST. If you have an example run that you would like specifically sped up, please send an email to the developers mailing list found here.