Title :
An SPMD-Like Algorithm for Parallelizing Molecular Dynamics Using OpenMP
Author :
Mingze Bai ; Shixin Sun ; Hong Tang ; Yusheng Dou ; Lo, Glenn V.
Author_Institution :
Univ. of Electron. Sci. & Technol. of China, Chengdu, China
Abstract :
The efficiency and scalability of early efforts to parallelize molecular dynamics calculations on shared-memory systems using OpenMP have been limited by attempts to avoid data race. Recent work has produced better performance, but involves significant revisions to the serial code. A new algorithm addresses these limitations.
Keywords :
molecular dynamics method; parallel processing; physics computing; shared memory systems; OpenMP; SPMD-like algorithm; molecular dynamics parallelization; shared-memory systems; single-program multiple-data parallelization; Biological system modeling; Computational modeling; Heuristic algorithms; Message systems; Molecular computing; Multicore processing; OpenMP; SPMD-like; molecular dynamics; parallel computing; single program multiple data; spatial decomposition;
Journal_Title :
Computing in Science & Engineering
DOI :
10.1109/MCSE.2012.66
