Abstract
Two force decomposition algorithms are proposed for parallelizing three-body interactions in Molecular Dynamics (MD) simulations. The first algorithm divides the entire 3D force matrix into equal sized force cubes that are assigned to parallel processors. In the second strategy, the force matrix is decomposed into slices of two-dimensional force matrixes, and those slices are distributed among processors cyclically. The proposed decomposition algorithms are implemented using MPI and tested in computational experiments. The performances of proposed decomposition methods are studied and compared with computational load theoretical analysis. Both theoretical prediction and computation experiments demonstrate that the load balance is a key factor that impacts the parallel performance of the examined system, and the cyclic force decomposition algorithm produced reasonably good overall performances.
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References
Bosko, J.T., Todd, B.D., Sadus, R.J.: Journal of Chemical Physics, 121, 1091–1096 (2004)
Rentsch, R., Brinksmeier, E., Li, J.: Nonlinear Dynamics of Production Systems, pp. 245–263. Wiley-VCH, Chichester (2003)
Plimpton, S.: Journal of Computational Physics 117, 1–19 (1995)
Roy, S., Jin, R.Y., Chaudhary, V., Hase, W.L.: Computer Physics Communications 128, 210–218 (2000)
Schreiber, H., Steinhauser, O., Schuster, P.: Parallel Computing 18, 557–573 (1992)
Smith, W.: Computer Physics Communications 62, 229–248 (1991)
Boyer, L.L., Pawley, G.S.: Journal of Computational Physics 78, 405–423 (1988)
Brunet, J.P., Edelman, A., Mesirov, J.P.: SIAM Journal of Scientific and Statistical Computing 14(5), 1143–1158 (1993)
Plimpton, S.: Journal of Computational Chemistry 17(3), 326–337 (1996)
Fincham, D.: Molecular Simulation, vol. 1, pp. 1–45 (1987)
Gupta, S.: Computer Physics Communications, vol. 70, pp. 243–270 (1992)
Matsuoka, O., Clement, E., Yoshimine, M.: Journal of Chemical Physics 64(4), 1351–1361 (1976)
Marcelli, G., Sadus, R.J.: Journal of Chemical Physics 111, 1533–1540 (1999)
Li, J., Zhou, Z., Sadus, R.J.: Modified Force Decomposition Strategies for Three-Body Interactions in Molecular Dynamics Simulations. Computer Physics Communications (to be published, 2006)
Axilrod, B.M., Teller, E.: Journal of Chemical Physics 11(6), 299–300 (1943)
Sadus, R.J.: Molecular Simulation of Fluids, Theory, Algorithms and Object-Orientation. Elsevier, Amsterdam (2002)
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Li, J., Zhou, Z., Sadus, R.J. (2006). Parallelization Algorithms for Three-Body Interactions in Molecular Dynamics Simulation. In: Guo, M., Yang, L.T., Di Martino, B., Zima, H.P., Dongarra, J., Tang, F. (eds) Parallel and Distributed Processing and Applications. ISPA 2006. Lecture Notes in Computer Science, vol 4330. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11946441_37
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DOI: https://doi.org/10.1007/11946441_37
Publisher Name: Springer, Berlin, Heidelberg
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