DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
文献类型：期刊论文
| 作者 | Zhang, Bo1; DeBuhr, Jackson1; Niedzielski, Drake2; Mayolo, Silvio3; Lu, Benzhuo4 ; Sterling, Thomas1
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| 刊名 | COMMUNICATIONS IN COMPUTATIONAL PHYSICS
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| 出版日期 | 2019-04-01 |
| 卷号 | 25期号:4页码:1235-1258 |
| 关键词 | Poisson-Boltzmann equation boundary element method DASHMM distributed computing |
| ISSN号 | 1815-2406 |
| DOI | 10.4208/cicp.OA-2018-0098 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000455963100013 |
| 出版者 | GLOBAL SCIENCE PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/32195]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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