New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.

Automated summary

This paper addresses the high performance extreme-scale molecular dynamics algorithm in the GENESIS software for cellular-scale MD simulations, achieving a performance of 8.30 ns/day on Fugaku supercomputer with a system containing 1.6 billion atoms, extending the size and time of MD simulations.