RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations

TL;DR

RPYFMM is a parallel adaptive fast multipole method software that efficiently computes biomolecular hydrodynamics interactions involving the Rotne-Prager-Yamakawa tensor, enabling large-scale simulations on supercomputers.

Contribution

It introduces a unified parallel implementation of the adaptive FMM for RPY tensor interactions, optimized for shared and distributed memory systems.

Findings

Can compute interactions for 15 million particles in one second

Achieves approximately 54% strong-scaling efficiency on 12,288 cores

Demonstrates scalability on a Cray XC30 cluster

Abstract

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) [1] where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library [2, 3]. Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12, 288 cores, while achieving approximately 54% strong-scaling efficiency.