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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 Hofinger
Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama 223-8522, Japan
Journal of Computational Chemistry, Vol. 30, No. 14. (15 November 2009), pp. 2351-2357.

@article{narumi2009current,

   title={Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach},

   author={Narumi, T. and Yasuoka, K. and Taiji, M. and H{\”o}finger, S.},

   journal={Journal of Computational Chemistry},

   volume={30},

   number={14},

   pages={2351–2357},

   year={2009},

   publisher={John Wiley & Sons}

}

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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 × for the largest problem studied. This type of alternative high performance computing can significantly improve the performance of demanding scientific applications. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
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