Simulative Analysis of a Multidimensional Torus-Based Reconfigurable Cluster for Molecular Dynamics

Molecular dynamics (MD) is a large-scale, communication-intensive problem that has been the subject of high-performance computing research and acceleration for years. Not surprisingly, the most success in accelerating MD comes from specialized systems such as the Anton machine. Our goal is to design a reconfigurable system that can accelerate MD while also being amenable to other communication-intensive applications. In this paper, we present a performance model for the 3D FFT kernel that forms the core of MD simulation on Anton. We validate the model against published Anton performance data and use the data to design and evaluate a similar interconnect for our existing Novo-G reconfigurable supercomputer. Through simulation studies, we predict that the upgraded machine will achieve nearly double the performance of Anton and fifty times that of established clusters like BlueGene/L for the 3D FFT kernel.