swMATH ID: 40371
Software Authors: Zhang, Bo; Debuhr, Jackson; Niedzielski, Drake; Mayolo, Silvio; Lu, Benzhuo; Sterling, Thomas
Description: DASHMM accelerated adaptive fast multipole Poisson-Boltzmann solver on distributed memory architecture. 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.
Homepage: https://arxiv.org/abs/1710.06316
Source Code:  https://github.com/zhang416/dafmpb
Keywords: Poisson-Boltzmann equation; boundary element method; DASHMM; distributed computing
Related Software: tabipb; VCMM; DASHMM; TABI; PyGBe; PBEQ-Solver; PAFMPB; TMSmesh; AFMPB; MIBPB; UHBD; APBS
Cited in: 1 Document

Citations by Year