Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

Pal, Anirban and Agarwala, Abhishek and Raha, Spumyendu and Bhattacharya, Baidurya (2014) Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions. In: JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 74 (3). pp. 2203-2214.

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Abstract

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Item Type:	Journal Article
Publication:	JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
Publisher:	ACADEMIC PRESS INC ELSEVIER SCIENCE
Additional Information:	copyright for this article belongs to ACADEMIC PRESS INC ELSEVIER SCIENCE,USA
Keywords:	Hybrid programming; Molecular dynamics; Message passing; OpenMP threading; Parallel computing
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	16 Mar 2014 11:20
Last Modified:	16 Mar 2014 11:21
URI:	http://eprints.iisc.ac.in/id/eprint/48623

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