NAMD: A Case Study in Multilingual Parallel Programming

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.

Krishnan  Varadarajan, "Communication Library for Parallel Architectures",
Dept. of Computer Science, University of Illinois, 1999.

@InProceedings{NamdLCPC98,
  author =       "L. V. Kal{\'e} and M. Bhandarkar and R. Brunner and
                  N. Krawetz and J. Phillips and A. Shinozaki",
  title =       {NAMD: A Case Study in Multilingual Parallel Programming},
  hideeditor =       "Zhiyuan Li and Pen-Chung Yew and Siddharta
                  Chatterjee and Chua-Huang Huang and P. Sadayappan
                  and David Sehr",
  number =       1366,
  series =       "Lecture Notes in Computer Science",
  pages =        "367--381",
  booktitle =    "Languages and Compilers for Parallel Computing",
  year =         1998,
  publisher =    "Springer-Verlag"
}