Parallelization and performance tuning of molecular dynamics code with OpenMP

被引：4

作者：

白树仁 ^{[1
]}

冉丽萍 ^{[2
]}

鲁奎麟 ^{[3
]}

机构：

[1] High Performance Computing Center, Hunan University, Changsha 410012, China

[2] State Key Laboratory of Powder Metallurgy,Central South University,Changsha 410083,China

[3] Department of Applied Physics,Hunan University,Changsha 410082,China

来源：

Journal of Central South University of Technology(English Edition) | 2006年 / 03期

基金：

中国国家自然科学基金;

关键词：

system analysis; molecular dynamics; parallel computing; performance tuning; OpenMP;

D O I：

暂无

中图分类号：

TP391.4 [模式识别与装置];

学科分类号：

0811 ; 081101 ; 081104 ; 1405 ;

摘要：

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.

引用

页码：260 / 264

页数：5