DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture

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.