1. 电子科技大学 计算机科学与工程学院，成都 610054
2. 重庆邮电大学 高性能计算与应用研究所，重庆 400065
3. Department of Physical Sciences, Nicholls State University, Thibodaux, Louisiana 70310, USA
Performance analysis and improvement of parallel molecular dynamics algorithm based on OpenMP
BAI Ming-ze1,2,CHENG Li1,DOU Yu-sheng1,3,SUN Shi-xin2
1. Institute of High Performance Computing and Application, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
2. School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu Sichuan 610054, China
3. Department of Physical Sciences, Nicholls State University, Thibodaux, Louisiana 70310, USA
Abstract：To enhance the computing speed of the molecular dynamics simulations on the shared memory servers, the performance of parallel molecular dynamics program based on Open Multi-Processing (OpenMP) approach with the critical section method was analyzed and improved. After testing performance on a multi-core server, as well as the calculations of speedup and parallel efficiency, an optimized triangle method was developed. In this method, stationary atom sets were assigned to threads respectively, and the number of atoms increased stepwise, which made the threads arrive at critical sections at different time. The triangle method can efficiently halve the idle time in critical sections and therefore can significantly enhance the parallel performance.
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BAI Ming-ze CHENG Li DOU Yu-sheng SUN Shi-xin. Performance analysis and improvement of parallel molecular dynamics algorithm based on OpenMP. Journal of Computer Applications, 2012, 32(01): 163-166.
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