Effect of parallel processing and optimization techniques in molecular dynamics
Kenji Satou, Kenri Konno, Osamu Ohta, Kazunori Mikami, Keita Teranishi, Yoichi M. A. Yamada, Shinya Ohki · 2008
Molecular dynamics (MD) has been studied long time due to its attractive function of predicting structure of molecules. Though many studies reported improved algorithms, it is unclear to an end-user of MD software tool to choose appropriate computer architecture, type of parallel processing, and optimization options to compile and execute the tool. In this study, we tested various combinations of parallel processing and optimization options on four different computer architectures, i.e. a vector supercomputer, multi-processor supercomputer with shared and distributed memories, and a PC cluster. Experimental results revealed superiority of PC cluster against other expensive supercomputers.