Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems

被引：6

作者：

Alam, Sadaf R. ^{[1
]}

Agarwal, Pratul K. ^{[1
]}

Hampton, Scott S. ^{[1
]}

Ong, Hong ^{[1
]}

机构：

[1] Oak Ridge Natl Lab, Div Math & Comp Sci, Oak Ridge, TN USA

来源：

HIGH PERFORMANCE COMPUTING - HIPC 2008, PROCEEDINGS | 2008年 / 5374卷

关键词：

Multicore; Performance; Molecular Dynamics Simulation; HPC;

D O I：

10.1007/978-3-540-89894-8_15

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Multi-core processors introduce many challenges both at the system and application levels that need to be addressed in order to attain the best performance. In this paper, we study the impact of the multi-core technologies in the context of two scalable, production-level molecular dynamics simulation frameworks. Experimental analysis and observations in this paper provide for a better understanding of the interactions between the application and the underlying system features such as memory bandwidth, architectural optimization. and communication library implementation. In particular, we observe that parallel efficiencies could be as low as 50% on quad-core systems while a set of dual-core processors connected with a high speed interconnect can easily outperform the same number of cores on a socket or in a package. This indicates that certain modifications to the software stack and application implementations are necessary in order to fully exploit the performance of multi-core based systems.

引用

页码：131 / 141

页数：11

共 12 条

[1] Biomolecular simulations on petascale: promises and challenges [J].

Agarwal, Pratul K. ;

Alam, Sadaf R. .

SCIDAC 2006: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING, 2006, 46 :327-333

[2]

ALAM SR, 2006, ACM S PRINC PRACT PA

[3]

Alam SR, 2006, IEEE INT S WORKL CHA

[4]

*AMBER, MD BENCHM AMBER CHAR

[5]

*AMD, AMD OPT REV F

[6]

[Anonymous], HPC CHALL BENCHM

[7]

[Anonymous], Performance Application Programming Interface

[8]

Intel, INT MPI BENCHM

[9] AMBER, A PACKAGE OF COMPUTER-PROGRAMS FOR APPLYING MOLECULAR MECHANICS, NORMAL-MODE ANALYSIS, MOLECULAR-DYNAMICS AND FREE-ENERGY CALCULATIONS TO SIMULATE THE STRUCTURAL AND ENERGETIC PROPERTIES OF MOLECULES [J].

PEARLMAN, DA ;

CASE, DA ;

CALDWELL, JW ;

ROSS, WS ;

CHEATHAM, TE ;

DEBOLT, S ;

FERGUSON, D ;

SEIBEL, G ;

KOLLMAN, P .

COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :1-41

[10] FAST PARALLEL ALGORITHMS FOR SHORT-RANGE MOLECULAR-DYNAMICS [J].

PLIMPTON, S .

JOURNAL OF COMPUTATIONAL PHYSICS, 1995, 117 (01) :1-19

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