Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced poisson boltzmann approach

Tetsu Narumi; Kenji Yasuoka; Makoto Taiji; Siegfried Höfinger

doi:10.1002/jcc.21257

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced poisson boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Höfinger

Department of Mechanical Engineering

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

Abstract

Scientific applications do frequently suffer from limited compute performance. In this article, we investigate the suitability of specialized computer chips to overcome this limitation. An enhanced Poisson Boltzmann program is ported to the graphics processing unit and the application specific integrated circuit MDGRAPE-3 and resulting execution times are compared to the conventional performance obtained on a modern central processing unit. Speed Up factors are measured and an analysis of numerical accuracy is provided. On both specialized architectures the improvement is increasing with problem size and reaches up to a Speed Up factor of 39 x for the largest problem studied. This type of alternative high performance computing can significantly improve the performance of demanding scientific applications.

Original language	English
Pages (from-to)	2351-2357
Number of pages	7
Journal	Journal of Computational Chemistry
Volume	30
Issue number	14
DOIs	https://doi.org/10.1002/jcc.21257
Publication status	Published - 2009 Nov 15

Keywords

ASIC
GPU
Implicit solvation models
MDGRAPE-3
Poisson boltzmann
Solvation

ASJC Scopus subject areas

Chemistry(all)
Computational Mathematics

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10.1002/jcc.21257

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