RPYFMM: Parallel adaptive fast multipole method for Rotne–Prager–Yamakawa tensor in biomolecular hydrodynamics simulations

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) (Greengard and Rokhlin, 1997) 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 (DeBuhr et al., 2016, 2018). 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. Program summaryProgram Title: RPYFMM: Parallel Adaptive FMM for RPY TensorProgram Files doi:http://dx.doi.org/10.17632/zpbjvy8whp.1Licensing provisions: BSD 3-clauseProgramming language: C++Nature of problem: Evaluate the Rotne–Prager–Yamakawa tensor matrix–vector multiplications describing the hydrodynamics interaction in biomolecular systems.Solution method: The Rotne–Prager–Yamakawa tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the new version of adaptive fast multipole method [1].Additional Comments: RPYFMM is built on top of the DASHMM library and the Asynchronous Multi-Tasking HPX-5 runtime system. DASHMM is automatically downloaded during installation and HPX-5 is available at http://hpx.crest.iu.edu/.