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

TL;DR

This paper introduces an enhanced AFMPB package that leverages the DASHMM library to enable distributed memory computation, significantly accelerating molecular solvation energy calculations for large systems.

Contribution

The paper presents the integration of DASHMM into AFMPB, allowing efficient distributed memory computations for large-scale molecular systems.

Findings

Handled a dengue virus system with over one million atoms

Reduced computation time from 10 hours to less than 30 seconds

Demonstrated scalability on a 12,288-core Cray XC30 cluster

Abstract

We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed memory computers. As a result, the new version can easily handle larger molecules or situations with higher accuracy requirements. To demonstrate the updated code, we applied the new version to a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles, and were able to reduce the time-to-solution from 10 hours reported in the previous release on a shared memory computer to less than 30 seconds on a Cray XC30 cluster using 12, 288 cores.