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International Workshop on Languages and Compilers for Parallel Computing

LCPC 1997: Languages and Compilers for Parallel Computing pp 367–381Cite as

NAMD: A case study in multilingual parallel programming

  • Parallel Programming Methods and Language Extensions
  • Conference paper
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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1366))

Abstract

Parallel languages are tools for constructing efficient application programs, while reducing the required labor. In this light, using the most appropriate tool for each component of a complex system seems natural, resulting in multi-paradigm multilingual programming. The Converse system developed at Illinois addresses the issues involved in supporting multilingual applications. This paper describes the development of a large parallel application in Computational Biophysics from the point of view of multilingual programming. NAMD, a molecular dynamics program, is implemented using three different “paradigms”: Parallel message-driven objects, Message-Passing, and Multithreading. The issues faced in implementing such a system, and the advantages of multilingual approach are discussed. NAMD is already operational on many parallel machines. Some preliminary performance results are presented and the lessons learned from this experience are discussed.

This work was supported in part by National Institutes of Health (NIH PHS 5 P41 RR05969-04 and NIH HL 16059) and National Science Foundation (NSF/GCAG BIR 93-18159 and NSF BIR 94-23827EQ). In addition, J. Phillips was supported by Computational Science Graduate Fellowship from United States Department of Energy.

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Authors and Affiliations

  1. Dept. of Computer Science, and Theoretical Biophysics Group, Beckman Institute, University of Illinois, 61801, Urbana, Illinois

    L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips & A. Shinozaki

Authors
  1. L. V. Kalé
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  2. M. Bhandarkar
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  3. R. Brunner
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  4. N. Krawetz
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  5. J. Phillips
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  6. A. Shinozaki
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Editor information

Zhiyuan Li Pen-Chung Yew Siddharta Chatterjee Chua-Huang Huang P. Sadayappan David Sehr

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© 1998 Springer-Verlag Berlin Heidelberg

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Kalé, L.V., Bhandarkar, M., Brunner, R., Krawetz, N., Phillips, J., Shinozaki, A. (1998). NAMD: A case study in multilingual parallel programming. In: Li, Z., Yew, PC., Chatterjee, S., Huang, CH., Sadayappan, P., Sehr, D. (eds) Languages and Compilers for Parallel Computing. LCPC 1997. Lecture Notes in Computer Science, vol 1366. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0032705

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  • DOI: https://doi.org/10.1007/BFb0032705

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-64472-9

  • Online ISBN: 978-3-540-69788-6

  • eBook Packages: Springer Book Archive

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