Determining the structure of biological macromolecules such as proteins and nucleic acids is an important element of molecular biology because of the intimate relation between form and function of these molecules. Individual sources of data about molecular structure are subject to varying degrees of uncertainty. Previously we have examined the parallelization of a probabilistic algorithm for combining multiple sources of uncertain data to estimate the three-dimensional structure of molecules and also predict a measure of the uncertainty in the estimated structure. In this paper we extend our work on two major fronts. First we present a hierarchiacal decomposition of the original algorithm which reduces the sequential computational complexity tremendously. The hierarchical decomposition in turn reveals a new axis of parallelism not present in the "flat" organization of the problems, as well as new parallelization problems. We demonstrate good speedups on two cache-coherent shared-memory multiprocessors, the Stanford DASH and the SGI Challenge, with distributed and centralized memory organization, respectively. Our results point to several areas of further study to make both the hierarchiacal and the parallel aspects more flexible for general problems: automatic structure decomposition, processor load balancing across the hierarchy, and data locality management in conjunction with load balancing. Finally we outline the directions we are investigating to incorporate these extensions.
机译:分层块匹配运动估计的多价并行化
机译:<![CDATA [使用分层结构CUO @ TIO
机译:分配和征服密度函数紧密分子动力学和元动力模拟的分层并行化
机译:并行分层分子结构估计
机译:匹配以减少层次结构化合成队列设计数据的治疗效果估计中的偏倚。
机译:更正:人口分布分析揭示了分子内在平行内吞途径的玩家的层次结构。
机译:并行分层分子结构估计