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Scalable parallel performance optimization of the gene sequence analyzing software Hmmpfam. (Chinese. English summary) Zbl 1107.68392

Summary: A scalable parallel MPI (Message Passing Interface) version of the popular protein structure prediction tool Hmmpfam is presented which is one of the kernel programs in the HMMER package. The master process in the previous PVM (Parallel Virtual Machine) version is a communication bottleneck, and the speedup will decrease rapidly when running on large scale parallel systems. A novel three-level communication structure is presented, by which the parallel processing at sequence level and HMM model level is obtained in both. Meanwhile, the load-balance strategies to sequence level and HMM model level distribution are provided separately. Since disk access for getting HMM model costs very much, a so-called “once load” strategy is provided to reduce the cost.

MSC:

68N19 Other programming paradigms (object-oriented, sequential, concurrent, automatic, etc.)
68U99 Computing methodologies and applications
92D20 Protein sequences, DNA sequences

Software:

PVM; Hmmpfam
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