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

Research output: Contribution to journalArticle

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 languageEnglish
Pages (from-to)2351-2357
Number of pages7
JournalJournal of Computational Chemistry
Volume30
Issue number14
DOIs
Publication statusPublished - 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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