Implementation and optimization of short-range molecular dynamics simulation on Hadoop
Hong Jun Tang · Computer Engineering and Science · 2013
Running molecular dynamics simulation programs on Hadoop has many research meanings such as saving hardware and software investment and shortening simulation time. However, Hadoop is not good at implementing the quick iteration and communication between sub-tasks in these scientific computing applications. Base on atom-decomposition method, the paper proposes three solutions and implements the parallel algorithm of molecular dynamics simulation by using HDFS read/write synchronization method. We tested it on a Hadoop cluster and analyzed expansibility, speed-up ratio and cost-time of various parts, and then obtained good results as high as 28x speedup in large-scale system simulations. The experiment results show molecular dynamics simulation on Hadoop is more economical and practical.