TY - JOUR
T1 - DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
AU - Bo Zhang, Jackson DeBuhr, Drake Niedzielski, Silvio Mayolo, Benzhuo Lu & Thomas Sterling
JO - Communications in Computational Physics
VL - 4
SP - 1235
EP - 1258
PY - 2018
DA - 2018/12
SN - 25
DO - http://doi.org/10.4208/cicp.OA-2018-0098
UR - https://global-sci.org/intro/article_detail/cicp/12897.html
KW - Poisson-Boltzmann equation, boundary element method, DASHMM, distributed computing.
AB - <p style="text-align: justify;">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.</p>