DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture

doi:10.4208/cicp.OA-2018-0098

	DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
	Zhang, Bo 1; DeBuhr, Jackson 1; Niedzielski, Drake 2; Mayolo, Silvio 3; Lu, Benzhuo4 ; Sterling, Thomas 1
	2019-04-01
发表期刊	COMMUNICATIONS IN COMPUTATIONAL PHYSICS
ISSN	1815-2406
卷号	25 期号:4 页码:1235-1258
摘要	We present DAFMPB (DASHMM-accelerated Adaptive Fast Multipole Poisson-Boltzmann solver) for rapid evaluation of the electrostatic potentials and forces, and total solvation-free energy in biomolecular systems modeled by the linearized Poisson-Boltzmann (LPB) equation. DAFMPB first reformulates the LPB into a boundary integral equation and then discretizes it using the node-patch scheme [33]. It solves the resulting linear system using GMRES, where it adopts the DASHMM library [14] to accelerate the matrix-vector multiplication in each iteration. DASHMM is built on top of a global address space allowing the user of DAFMPB to operate on both shared and distributed memory computers with modification of their code. This paper is a brief summary of the program, including the algorithm, implementation, installation and usage.
关键词	Poisson-Boltzmann equation boundary element method DASHMM distributed computing
DOI	10.4208/cicp.OA-2018-0098
语种	英语
资助项目	Science Challenge Project[TZ2016003] ; National Key Research and Development Program of China[2016YFB0201304] ; China NSF[NSFC 21573274] ; China NSF[11771435] ; National Science Foundation[ACI-1440396] ; National Science Foundation ; Lilly Endowment, Inc.
WOS研究方向	Physics
WOS类目	Physics, Mathematical
WOS记录号	WOS:000455963100013
出版者	GLOBAL SCIENCE PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/32196
专题	计算数学与科学工程计算研究所
通讯作者	Zhang, Bo
作者单位	1.Indiana Univ, Sch Informat Comp & Engn, Ctr Res Extreme Scale Technol, Bloomington, IN 47404 USA 2.Rensselaer Polytech Inst, Dept Phys, Troy, NY 12180 USA 3.Tennessee Technol Univ, Dept Comp Sci, Cookeville, TN 38505 USA 4.Chinese Acad Sci, Acad Math & Syst Sci, State Key Lab Sci Engn Comp, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Bo,DeBuhr, Jackson,Niedzielski, Drake,et al. DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture[J]. COMMUNICATIONS IN COMPUTATIONAL PHYSICS,2019,25(4):1235-1258.
APA	Zhang, Bo,DeBuhr, Jackson,Niedzielski, Drake,Mayolo, Silvio,Lu, Benzhuo,&Sterling, Thomas.(2019).DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture.COMMUNICATIONS IN COMPUTATIONAL PHYSICS,25(4),1235-1258.
MLA	Zhang, Bo,et al."DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture".COMMUNICATIONS IN COMPUTATIONAL PHYSICS 25.4(2019):1235-1258.