Molecular dynamics simulation: Implementation and optimization based on Hadoop

Abstract

At first the paper introduced the basic concept and mechanism of Hadoop architecture and the current parallel research situation of molecular dynamics simulation, then three solutions were proposed for implementing the parallel algorithm using atom-decomposition method on Hadoop to overcome shortcomings of fast iteration and communication among sub-tasks. After that tested and analyzed program's speed-up ratio, expansibility and cost-time of various parts, then did performance tuning in many ways, finally obtained good results as high as 28× speedup in large-scale system simulations. The test showing molecular dynamics simulation based on Hadoop is more economical and practical.