Parallelization and performance tuning of molecular dynamics code with OpenMP^①

来源期刊：中南大学学报(英文版)2006年第3期

论文作者：白树仁 鲁奎麟 冉丽萍

文章页码：260 - 264

Key words：system analysis; molecular dynamics; parallel computing; performance tuning; OpenMP;

Abstract: An OpenMP approach was proposed to parallelize the sequential molecular dynamics(MD) code on shared memory machines. When a code is converted from the sequential form to the parallel form, data dependence is a main problem. A traditional sequential molecular dynamics code is anatomized to find the data dependence segments in it, and the two different methods, i.e., recover method and backward mapping method were used to eliminate those data dependencies in order to realize the parallelization of this sequential MD code. The performance of the parallelized MD code was analyzed by using some performance analysis tools. The results of the test show that the computing size of this code increases sharply form 1 million atoms before parallelization to 20 million atoms after parallelization, and the wall clock during computing is reduced largely. Some hot-spots in this code are found and optimized by improved algorithm. The efficiency of parallel computing is 30% higher than that of before, and the calculation time is saved and larger scale calculation problems are solved.