Parallelizing Molecular Dynamics by Using Hybrid OpenMP and MPI on MultiCores Cluster

• Main Authors: JHOU GUO-WEI, 周國偉
• Other Authors: 洪榮泰
• Format: Others
• Language: zh-TW
• Published: 2010
• Online Access: http://ndltd.ncl.edu.tw/handle/77559727652583243160

碩士 === 中華科技大學 === 機電光工程研究所在職專班 === 98 === A hybrid MPI/OpenMP parallel technique for molecular dynamic simulations (MD) with short-range multi-body potential was presented. Due to the decreasing of performance as increasing the number of threads, the multicore computer cluster is used to improve the overall parallel efficiency in this work. In hybrid method, the atom is distributed into each computational node by domain decomposition method firstly. Secondly, the procedure of MD is taken by atomic decomposition method and the triple nested-loop in MD is calculated by OpenMP. To investigate the parallel efficiency with different computer architectures and parallel schemes, the code is executed on Intel Xeon 32 cores, AMD opetron 42 cores and multicore cluster. The efficiency is decreased as increasing the number of core with pure OpenMP and the efficiency kept a constant, near 80%, as increasing the number of cores. The parallel efficiency of MPI/OpenMP is higher than 80% with mulitcore computer and is 95% with cluster computer. That is higher that that of pure MPI and it worth noting the efficiency is kept at constant value by increasing the overall number of cores with having better scalability.