Volume 25, Issue 4
DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture

Bo Zhang, Jackson DeBuhr, Drake Niedzielski, Silvio Mayolo, Benzhuo Lu & Thomas Sterling

Commun. Comput. Phys., 25 (2019), pp. 1235-1258.

Published online: 2018-12

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  • 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.

  • Keywords

Poisson-Boltzmann equation boundary element method DASHMM distributed computing.

  • AMS Subject Headings

45B05 31C20 92C05 68N19

  • Copyright

COPYRIGHT: © Global Science Press

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@Article{CiCP-25-1235, author = {Bo Zhang, Jackson DeBuhr, Drake Niedzielski, Silvio Mayolo, Benzhuo Lu and Thomas Sterling}, title = {DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture}, journal = {Communications in Computational Physics}, year = {2018}, volume = {25}, number = {4}, pages = {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.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.OA-2018-0098}, url = {http://global-sci.org/intro/article_detail/cicp/12897.html} }
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