The author parallelized a tertiary structure search algorithm on a distributed memory parallel computer, Cenju-3, utilizing a standard message passing interface (MPI) parallel library. For parallelization scheme, a master-workers model is used. I analyzed the total performance by utilizing a M/M/1 queueing model and Jackson's model, and clearly explained the actual turn around times. Tertiary structure search is a computationally intensive task. When test sequences are distributed to all processors, a single key sequence can be tested independently. Thus high parallelization results are anticipated. Since database is allocated on a master processor, worker processors should acquire test sequences from the master processor. Sometimes a worker should wait until other workers obtain test sequences from the master processor. By this waiting, the total performance will saturate when the number of processors proceeds certain level. I analyzed the total performance by utilizing a M/M/1 queueing model and Jackson's model. By using these models, the actual turn around times are explained clearly.
Index Terms:
Performance analysis, Parallel machine Cenju-3, Genome information processing, Queuing model, and MPI
Citation:
Minoru Asogawa, "Parallel Tertiary Structure Search on the Cenju-3 Parallel Machine," ispan, pp.256, 1996 International Symposium on Parallel Architectures, Algorithms and Networks (ISPAN '96), 1996
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