A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

Abstract—As parallel algorithms and architectures drive the longest molecular dynamics (MD) simulations towards the millisecond scale, traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Inspired by the programming interface of Google’s MapReduce, we have built a new parallel analysis framework called HiMach, which allows users to write trajectory analysis programs sequentially, and carries out the parallel execution of the programs automatically. We introduce (1) a new MD trajectory data analysis model that is amenable to parallel processing, (2) a new interface for defining trajectories to be analyzed, (3) a novel method to make use of an existing sequential analysis tool called VMD, and (4) an extension to the original MapReduce model to support multiple rounds of analysis. Performance evaluations on up to 512 cores demonstrate the efficiency and scalability of the HiMach framework on a Linux cluster. I

Leveraging the Power of Big Data Tools for Large Scale Molecular Dynamics Analysis

International audienceParallel Molecular Dynamics simulations are generating atom trajectories of growing sizes and complexity. Analyzing these trajectories is expensive computationally and time consuming. One reason is the lack of tools that enable the computational biologist to easily implement the analysis while ensuring reduced processing times exploiting the benefits of parallel architectures. In this paper, we present a comparison between two parallel analytics frameworks based on the Map/Reduce paradigm: HiMach, a dedicated framework for trajectory analysis based on MPI, and Flink, a Big Data analytics framework. Both frameworks enable to hide the complexity of parallel code creation to the programmer, providing significant performance gains compared to a sequential execution