Links to MPI-HMMer
There is an early version available of MPI-HMMER which is a multiple-level optimization of the original HMMER 2.3.2 code by Sean Eddy of the HHMI Janelia Farms facility. This optimization provides multiple layers of acceleration, from micro-vectorization of the p7Viterbi algorithm through parallelization using MPI.
The hmmsearch and hmmpfam were refactored from PVM code into MPI code, and various hand optimization and code improvements were made. The resulting code demonstrates good speedup and high parallelism on low latency connected systems with low OS jitter. This new implementation is approximately 4x faster than the PVM version of HMMER, approximately 12x faster than the baseline single CPU tests.
http://downloads.scalableinformatics.com/downloads/mpihmmer/
http://code.google.com/p/mpihmmer/
HMMer
