Miller P L, Nadkarni P, Gelernter J E, Carriero N, Pakstis A J, Kidd K K
Yale University School of Medicine, New Haven, Connecticut 06510.
Comput Biomed Res. 1991 Jun;24(3):234-48. doi: 10.1016/0010-4809(91)90046-y.
Parallel computers offer a solution to improve the lengthy computation time of many conventional, sequential programs used in molecular biology. On a parallel computer, different pieces of the computation are performed simultaneously on different processors. LINKMAP is a sequential program widely used by scientists to perform genetic linkage analysis. We have converted LINKMAP to run on a parallel computer, using the machine-independent parallel programming language, Linda. Using the parallelization of LINKMAP as a case study, the paper outlines an approach to converting existing highly iterative programs to a parallel form. The paper describes the steps involved in converting the sequential program to a parallel program. It presents performance benchmarks comparing the sequential version of LINKMAP with the parallel version running on different parallel machines. The paper also discusses alternative approaches to the problem of "load balancing," making sure the computational load is shared as evenly as possible among the available processors.
并行计算机为解决分子生物学中许多传统顺序程序计算时间过长的问题提供了一种方案。在并行计算机上，不同的计算部分可在不同处理器上同时执行。LINKMAP是科学家广泛用于进行遗传连锁分析的顺序程序。我们已使用与机器无关的并行编程语言Linda将LINKMAP转换为可在并行计算机上运行。以LINKMAP的并行化作为案例研究，本文概述了一种将现有高度迭代程序转换为并行形式的方法。本文描述了将顺序程序转换为并行程序所涉及的步骤。它给出了性能基准，比较了LINKMAP的顺序版本与在不同并行机器上运行的并行版本。本文还讨论了“负载平衡”问题的替代方法，确保计算负载在可用处理器之间尽可能均匀地共享。
