TY - JOUR
T1 - RPYFMM: Parallel adaptive fast multipole method for Rotne–Prager–Yamakawa tensor in biomolecular hydrodynamics simulations
AU - Guan, W.
AU - Cheng, X.
AU - Huang, J.
AU - Huber, G.
AU - Li, W.
AU - McCammon, J. A.
AU - Zhang, B.
N1 - 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.
PY - 2018/2/16
Y1 - 2018/2/16
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/678752
UR - https://linkinghub.elsevier.com/retrieve/pii/S001046551830033X
UR - http://www.scopus.com/inward/record.url?scp=85042474536&partnerID=8YFLogxK
U2 - 10.1016/j.cpc.2018.02.005
DO - 10.1016/j.cpc.2018.02.005
M3 - Article
C2 - 30147116
SN - 0010-4655
VL - 227
SP - 99
EP - 108
JO - Computer Physics Communications
JF - Computer Physics Communications
ER -