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

Access to Document

10.1002/jcc.21257

Cite this

@article{88e30216867e454d86315324ac856e2e,

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

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.",

keywords = "ASIC, GPU, Implicit solvation models, MDGRAPE-3, Poisson boltzmann, Solvation",

author = "Tetsu Narumi and Kenji Yasuoka and Makoto Taiji and Siegfried H{\"o}finger",

year = "2009",

month = nov,

day = "15",

doi = "10.1002/jcc.21257",

language = "English",

volume = "30",

pages = "2351--2357",

journal = "Journal of Computational Chemistry",

issn = "0192-8651",

publisher = "John Wiley and Sons Inc.",

number = "14",

}

TY - JOUR

T1 - Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced poisson boltzmann approach

AU - Narumi, Tetsu

AU - Yasuoka, Kenji

AU - Taiji, Makoto

AU - Höfinger, Siegfried

PY - 2009/11/15

Y1 - 2009/11/15

N2 - 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.

AB - 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.

KW - ASIC

KW - GPU

KW - Implicit solvation models

KW - MDGRAPE-3

KW - Poisson boltzmann

KW - Solvation

UR - http://www.scopus.com/inward/record.url?scp=70349459442&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349459442&partnerID=8YFLogxK

U2 - 10.1002/jcc.21257

DO - 10.1002/jcc.21257

M3 - Article

C2 - 19350574

AN - SCOPUS:70349459442

VL - 30

SP - 2351

EP - 2357

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 14

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this