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

W. Guan, X. Cheng, J. Huang, G. Huber, W. Li, J. A. McCammon, B. Zhang

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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.
Original languageEnglish (US)
Pages (from-to)99-108
Number of pages10
JournalComputer Physics Communications
Volume227
DOIs
StatePublished - Feb 16 2018
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-08
Acknowledgements: The authors gratefully acknowledge the inspiring discussions with Profs. David Keyes and Rio Yokota on different parallelization strategies for our solver. BZ was supported in part by National Science Foundation Grant Number ACI-1440396. GH was supported in part by National Institute of Health Grant Number GM 31749. This research was supported in part by Lilly Endowment, Inc., through its support for the Indiana University Pervasive Technology Institute. Part of the work was finished when JH was a visiting professor at the King Abdullah University of Science and Technology.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

Fingerprint

Dive into the research topics of 'RPYFMM: Parallel adaptive fast multipole method for Rotne–Prager–Yamakawa tensor in biomolecular hydrodynamics simulations'. Together they form a unique fingerprint.

Cite this