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

摘要

RPYFMM is a software package for the efficient evaluation of the potentialfield governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions inbiomolecular hydrodynamics simulations. In our algorithm, the RPY tensor isdecomposed as a linear combination of four Laplace interactions, each of whichis evaluated using the adaptive fast multipole method (FMM) [1] where theexponential expansions are applied to diagonalize the multipole-to-localtranslation operators. RPYFMM offers a unified execution on both shared anddistributed memory computers by leveraging the DASHMM library [2, 3].Preliminary numerical results show that the interactions for a molecular systemof 15 million particles (beads) can be computed within one second on a CrayXC30 cluster using 12, 288 cores, while achieving approximately 54%strong-scaling efficiency.