DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
Year: 2019
Author: Bo Zhang, Jackson DeBuhr, Drake Niedzielski, Silvio Mayolo, Benzhuo Lu, Thomas Sterling
Communications in Computational Physics, Vol. 25 (2019), Iss. 4 : pp. 1235–1258
Abstract
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.
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Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/10.4208/cicp.OA-2018-0098
Communications in Computational Physics, Vol. 25 (2019), Iss. 4 : pp. 1235–1258
Published online: 2019-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 24
Keywords: Poisson-Boltzmann equation boundary element method DASHMM distributed computing.
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