Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-Enabled Molecular Dynamics Simulations
Samuel Schlachter, Stephen Herbein, Shu Ou, Jeremy S. Logan, Sandeep A. Patel, Michela Taufer · IEEE Design and Test · 2013
To address the challenge of pursuing coordinated trajectory progression and efficient resource utilization of GPU-enabled molecular dynamics (MD) simulations on nondedicated high-end clusters, our work aims to supplement, rather than rewrite, existing workflow and resource managers. To this end, we propose a companion module that complements workflow managers and a wrapper module that supports resource managers. We model the maximum utilization of our approach in comparison to the traditional common approach for two molecular simulations: a sodium dodecyl sulfate (SDS) system with dynamically variable job runtimes and a carbon nanotube system with hardware and application failures. In light of our solution, we estimate increased utilization in both simulations. These findings implicitly assure a more coordinated progression of long trajectories across GPUs on a cluster's nodes.