Parallel tertiary structure search on the Cenju-S parallel machine

The author parallelized a tertiary structure search algorithm on a distributed memory parallel computer, Cenju-S, utilizing a standard message passing interface (MPI) parallel library. For parallelization scheme, a master-workers model is used. The author 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.