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arXiv · 1710.06316

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

B. Zhang·J. DeBuhr·D. Niedzielski·S. Mayolo·B. Lu·T. Sterling
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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.

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B. Zhang, J. DeBuhr, D. Niedzielski, S. Mayolo, B. Lu, T. Sterling. 2017-10-17. DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture. https://arxiv.org/abs/1710.06316

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