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DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
Zhang, Bo1; DeBuhr, Jackson1; Niedzielski, Drake2; Mayolo, Silvio3; Lu, Benzhuo4; Sterling, Thomas1
2019-04-01
Source PublicationCOMMUNICATIONS IN COMPUTATIONAL PHYSICS
ISSN1815-2406
Volume25Issue:4Pages:1235-1258
AbstractWe 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.
KeywordPoisson-Boltzmann equation boundary element method DASHMM distributed computing
DOI10.4208/cicp.OA-2018-0098
Language英语
Funding ProjectScience 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 Research AreaPhysics
WOS SubjectPhysics, Mathematical
WOS IDWOS:000455963100013
PublisherGLOBAL SCIENCE PRESS
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/32196
Collection计算数学与科学工程计算研究所
Affiliation1.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
Recommended Citation
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.
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