Computational Technology Resources - CCP

Keywords: DL_POLY, molecular dynamics, high performance computing, I/O, load balancing, software.

Summary

Molecular dynamics has become a major tool in academic and industrial research in areas as varied as chemistry, biochemistry, physics and material science. For this reason there is a constant need for developments improving the utilisation of supercomputer resources. The availability of such resources has raised the demand for access to longer time- and length-scales. On the one hand this has introduced new methodologies such as hyper-dynamics and meta-dynamics and on the other it has pushed development of software engineering and numerical methods to utilise resources more efficiently. An example of a software project that addresses such demands is DL_POLY_3. The code development has placed a particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of order of hundreds of millions particles and beyond. In this paper we discuss the practical challenges to performance and scalability in research. These involve development of an efficient I/O scheme as the first step in accessing longer time- and length-scales. We also discuss the problems of tackling systems with highly non-uniform particle density distribution by spatial domain decomposition methods and outline a novel methodology that can load balance such systems.

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Front Page Browse CCP CSETS CTR IJRT Other Authors Search Purchase Guide FAQ Contact us	Civil-Comp Proceedings ISSN 1759-3433 CCP: 90 PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON PARALLEL, DISTRIBUTED AND GRID COMPUTING FOR ENGINEERING Edited by: Paper 3 Challenges in Molecular Dynamics on a Grand Scale I.T. Todorov¹, W. Smith¹, I.J. Bush² and L. Ellison¹ ¹CSE Department, STFC Daresbury Laboratory, Warrington, United Kingdom ²NAG Ltd., Oxford, United Kingdom doi:10.4203/ccp.90.3 purchase the full-text of this paper Full Bibliographic Reference for this paper I.T. Todorov, W. Smith, I.J. Bush, L. Ellison, "Challenges in Molecular Dynamics on a Grand Scale", in , (Editors), "Proceedings of the First International Conference on Parallel, Distributed and Grid Computing for Engineering", Civil-Comp Press, Stirlingshire, UK, Paper 3, 2009. doi:10.4203/ccp.90.3 Keywords: DL_POLY, molecular dynamics, high performance computing, I/O, load balancing, software. Summary Molecular dynamics has become a major tool in academic and industrial research in areas as varied as chemistry, biochemistry, physics and material science. For this reason there is a constant need for developments improving the utilisation of supercomputer resources. The availability of such resources has raised the demand for access to longer time- and length-scales. On the one hand this has introduced new methodologies such as hyper-dynamics and meta-dynamics and on the other it has pushed development of software engineering and numerical methods to utilise resources more efficiently. An example of a software project that addresses such demands is DL_POLY_3. The code development has placed a particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of order of hundreds of millions particles and beyond. In this paper we discuss the practical challenges to performance and scalability in research. These involve development of an efficient I/O scheme as the first step in accessing longer time- and length-scales. We also discuss the problems of tackling systems with highly non-uniform particle density distribution by spatial domain decomposition methods and outline a novel methodology that can load balance such systems. purchase the full-text of this paper (price £20) go to the previous paper go to the next paper return to the table of contents return to the book description purchase this book (price £72 +P&P)
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