Abstract
We propose an approach for partitioning an irregular application problem in computational biology called Molecular Dynamics (MD) of Macromolecules. We model the application as a task graph which we call a compact MD graph. Such a modeling allows existing mapping heuristics to be applied to this problem. We then provide a parallel algorithm for this application, by using an efficient mapping heuristic called Allocation By Recursive Mincut (ARM) to map the compact MD graph to a hypercube connected parallel computer, the nCUBE 2S. A canonical model for executing parallel computations modeled as graphs is described. Thus, we attempt to provide the missing link between the mapping research and application implementation research, and demonstrate that the execution time can be sufficiently reduced by considering formal mapping techniques, while designing parallel programs for important applications.
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