Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach.
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.
Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama 223-8522, Japan.
Tetsu
T
Narumi
Kenji
K
Yasuoka
Makoto
M
Taiji
Siegfried
S
Höfinger