Paper Citing NAMD - Abstract
Yin, Qian; Luo, Ruiyi; Guo, Ping
Parallelization and Optimization of Molecular Dynamics Simulation on Many Integrated Core
PROCEEDINGS OF THE 2012 EIGHTH INTERNATIONAL CONFERENCE ON COMPUTATIONAL INTELLIGENCE AND SECURITY (CIS 2012), 209-213, 2012
Molecular dynamics (MD) simulations are useful in various areas. In this paper, we parallelize and optimize the grid-based MD algorithm on Many Integrated Core (MIC) Architecture. To get full play of the hardware and accelerate computation of MD simulation, we design the parallel structure using multi-threads with OpenMP. Also, various or method such as Array Notification, intrinsic and so on are used to vectorize the application according to the character of MIC for a higher performance. Due that multi-core is also a trendy of CPU and High Performance Computing, our method can be followed by other similar applications and provide a more choice.
