Study of Optimal Parallel Computation for Molecular Dynamics

• Main Authors: Banjamin Dong, 董仲桓
• Other Authors: C. S. wang
• Format: Others
• Language: zh-TW
• Published: 2003
• Online Access: http://ndltd.ncl.edu.tw/handle/94298481022512778528

碩士 === 國立臺北科技大學 === 機電整合研究所 === 91 === The thesis use PC Cluster and Parallel computational PROM algorithms to reduce the CPU time of Molecular Dynamics program of “ar.for” that is modified by NTFL lab. The PC Cluster system, composed by two PC, runs by Linux OS kernel. By using MPICH (message transfer interface program) and FORTRAN compiler language to recompose the sequence code as parallel code We develop the PROM algorithms, including Parallization, Ram sequence continue, Optimization of anti-symmetric matrix, and Manipulation transfer buffer zone. It can save both the computational CPU time and the transfer time in buffer zone. We explored the CPU time, data exchange time and the parallel efficiency by our PROM algorithm. There are two important tasks to reduce the CPU time and transfer time. Firstly, by packing transfer data or replace transfer with calculation. Secondly, by balancing the calculation load for both CPU which runs the parallel program. By utilizing PROM algorithms, the CPU time will be reduced to 24.4% which is compared with original code