Breaking the Molecular Dynamics Timescale Barrier Using a Wafer-Scale System
Kylee Santos, Stan Moore, Tomas Oppelstrup, A Sharifian, Ilya Sharapov, A.L. Thompson, Delyan Z. Kalchev, Danny Pérez, Robert D. Schreiber, Scott Pakin, Edgar A. León, James H. Laros, Michael James, Sivasankaran Rajamanickam
Abstract
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale supercomputers, however, runtimes are excessive for systems and timescales of scientific interest. Here, we demonstrate strong scaling of MD simulations on the Cerebras Wafer-Scale Engine. By dedicating a processor core for each simulated atom, we demonstrate a 457-fold improvement in timesteps per second versus the Frontier GPU-based Exascale platform, along with a large improvement in timesteps per unit energy. Reducing every year of runtime to less than a day unlocks currently inaccessible timescales of slow microstructure transformation processes that are critical for understanding material behavior and function.Our dataflow algorithm runs Embedded Atom Method (EAM) simulations at rates over 699k timesteps per second for problems with up to 800k atoms. This demonstrated performance is unprecedented for general-purpose processing cores.