Parallel molecular dynamics simulations of alkane/hydroxylated α-aluminum oxide interfaces

S. Roy; R. Y. Jin; V. Chaudhary; W. L. Hase

doi:10.1016/S0010-4655(00)00040-0

Parallel molecular dynamics simulations of alkane/hydroxylated α-aluminum oxide interfaces

S. Roy, R. Y. Jin, V. Chaudhary, W. L. Hase

Chemistry and Biochemistry

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

In this paper we describe a practical implementation of parallel computation for the molecular dynamics (MD) simulation of an alkane/aluminum oxide interface. A serial MD program was converted into a parallel code utilizing the message passing interface (MPI). This code was evaluated on a twelve processor symmetrical multiprocessor as well as on a cluster of four processor SMPs. A maximum speedup of 5.25 was achieved with twelve processors on the large shared memory machine. The cluster performance saturated at a speedup of 4.5 with two nodes. High communication costs and considerable load imbalance in the system were identified as areas that need further investigation for obtaining better performance.

Original language	English
Pages (from-to)	210-218
Number of pages	9
Journal	Computer Physics Communications
Volume	128
Issue number	1
DOIs	https://doi.org/10.1016/S0010-4655(00)00040-0
State	Published - Jun 9 2000

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abstract = "In this paper we describe a practical implementation of parallel computation for the molecular dynamics (MD) simulation of an alkane/aluminum oxide interface. A serial MD program was converted into a parallel code utilizing the message passing interface (MPI). This code was evaluated on a twelve processor symmetrical multiprocessor as well as on a cluster of four processor SMPs. A maximum speedup of 5.25 was achieved with twelve processors on the large shared memory machine. The cluster performance saturated at a speedup of 4.5 with two nodes. High communication costs and considerable load imbalance in the system were identified as areas that need further investigation for obtaining better performance.",

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note = "Funding Information: I This work was supported in part by grants from Ford Motor Company, the Office of Naval Research, and National Science Foundation. II This paper is published as part of a thematic issue on Parallel Computing in Chemical Physics. ∗Corresponding author. E-mail: wlh@chem.wayne.edu.",

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Parallel molecular dynamics simulations of alkane/hydroxylated α-aluminum oxide interfaces

Abstract

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