A Hierarchical Approach for Parallelization of a Global Optimization Method for Protein Structure Prediction

Authors:
Silvia A. Crivelli;T. Head-Gordon;Richard H. Byrd;Elizabeth Eskow;Robert B. Schnabel
Affiliations:
-;-;-;-;-
Venue:
Euro-Par '99 Proceedings of the 5th International Euro-Par Conference on Parallel Processing
Year:
1999

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Abstract

We discuss the parallelization of our protein structure prediction algorithm on distributed-memory computers. Because the computation can be represented as a search through a vast tree of possible solutions, a hierarchical approach that assigns subtrees to different groups of processors allows us to partition the work efficiently and maintain information updated without incurring significant communication overhead. Our results show that a dynamic strategy for load balancing outperforms the static one.