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Software: Announcing MPI-HMMER
Submitted by Joe Landman; posted on Friday, January 05, 2007 (1 comment)
The MPI-HMMER team is pleased to announce the release of MPI-HMMER. MPI-HMMER is a multiple-level optimization of the original HMMER 2.3.2 code by Sean Eddy of the HHMI Janelia Farms facility. Our implementation consists of two distinct optimizations: a portably tuned P7Viterbi function as well as an MPI implementation. Our MPI implementation is based on the original PVM HMMER code, with enhancements to improve the scalability and I/O of both hmmpfam and hmmsearch. Both optimizations are independent of one another, allowing future enhancements to be easily added and tested. The MPI implementation exhibits excellent speedups over the base PVM implementation. Further, we provide a verification mode in both hmmpfam and hmmsearch that ensures (at a cost of speed) results are returned in exactly the same order as the serial version.

Our code has been tested for stability up to 256 nodes, but should scale to as many nodes as the master node's memory allows.


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mpi BLAST Question
Submitted by Saul Kravitz; posted on Wednesday, December 17, 2008
We are having trouble running the mpiBLAST formatDB on large (nraa-size) sequence collections. If you routinely succeed at this, could you contact me please? Thx, Saul Kravitz
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