Abstract
This chapter describes the parallelization of GROMOS96, a molecular dynamics simulation code, on SCI-interconnected cluster architectures.
The simulation of the dynamics of molecular systems is one of the central topics in scientific high-performance computing. It has been subject to parallel processing already for a long time. GROMOS96 [16] is a well-known code in this area with a quite long history. It is the successor of GROMOS87, which has been re-designed for improved functionality and performance, including a parallel implementation for shared memory Silicon Graphics multiprocessors [7].
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References
Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Oxford University Press, Oxford (1987)
Bugge, H.O., Husoy, P.O.: Efficient SAR processing on the Scali System. In: Proc. IPPS (1997)
Clark, T.W., von Hanxleden, R., McCammon, J.A., Scott, L.R.: Parallelizing Molecular Dynamics using Spatial Decomposition. In: Proc. Scalable High Perf. Comp. Conf. (1994)
Dormanns, M., Lankes, S., Bemmerl, T., Bolz, G., Pfeiffle, E.: Parallelization of an Airline Flight-Scheduling Module on a SCI-Coupled NUMA Shared-Memory Cluster. In: Proc. High Perf. Computing Systems and Applications (HPCS), Kingston, Canada (1999)
Dormanns, M., Sprangers, W., Ertl, H., Bemmerl, T.: A Programming Interface for NUMA Shared-Memory Clusters. In: Hertzberger, B., Sloot, P.M.A. (eds.) HPCN-Europe 1997. LNCS, vol. 1225, pp. 698–707. Springer, Heidelberg (1997)
Green, D.G., Meacham, K.E., van Hoesel, F.: Parallelization of the molecular dynamics code GROMOS87 for distributed memory parallel architectures. In: Waśniewski, J., Dongarra, J. (eds.) PARA 1994. LNCS, vol. 879, pp. 875–879. Springer, Heidelberg (1994)
GROMOS96 benchmark results: http://igc.ethz.ch/gromos/benchmark.html
Heiß, H.-U., Dormanns, M.: Partitioning and Mapping of Parallel Programs by Self-Organization. Concurrency: Practice & Experience 8(9), 685–706 (1996)
Lam, M.S., Rothberg, E.E., Wolf, M.E.: The Cache Performance of Blocked Algorithms. In: Proc. 4th. Int. Conf. on Architectural Support for Programming Languages and Operating Systems, ASPLOS IV (1991)
Lupo, J.A.: Benchmarking UHGROMOS. In: Proc. 28th Int. Conf. on System Sciences, pp. 132–141 (1995)
Meacham, K., Green, D.: Parallelization of the GROMOS87 Molecular Dynamics Code: An Update. In: Liddell, H., Colbrook, A., Hertzberger, B., Sloot, P.M.A. (eds.) HPCN-Europe 1996. LNCS, vol. 1067, pp. 170–176. Springer, Heidelberg (1996)
National Center for Supercomputing Applications: Computational Biology Applications, UHGROMOS and Gromos87 Benchmarks, http://mithril.ncsa.uiuc.edu/SCD/straka/PerfAnalysis/Apps/cb.html
Paas, S.M., Dormanns, M., Bemmerl, T., Scholtyssik, K., Lankes, S.: Computing on a Cluster of PCs: Project Overview and Early Experiences. 1. Workshop Cluster Computing, Technical Report CSR-97-05, TU Chemnitz, Dept. of Computer Science (1997)
Stockhausen, M.: Parallelisierung und Evaluation eines Rechenkerns einer Erdbebensimulation auf einem speichergekoppeltem PC-Cluster. Diploma Thesis (in German), Chair for Operating Systems, RWTH Aachen (1999)
Tholen, S.: Parallelisierung raumakustischer Simulationsalgorithmen für SCI Cluster. Diploma Thesis (in German), Chair for Operating Systems, RWTH Aachen (1998)
van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G.: Biomolecular Simulation: The GROMOS96 Manual and User Guide. BIOMOS b.v., Zürich, Groningen and VDF Hochschulverlag AG an der ETH Zürich (1996)
Warren, M.S., Becker, D.J., Goda, M.P., Salmon, J.K., Sterling, T.: Parallel Supercomputing with Commodity Components. In: Proc. Int. Conf. on Parallel and Distributed Processing Techniques and Applications (PDPTA), pp. 1372–1381 (1997)
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Dormanns, M. (1999). Shared Memory Parallelization of the GROMOS96 Molecular Dynamics Code. In: Hellwagner, H., Reinefeld, A. (eds) SCI: Scalable Coherent Interface. Lecture Notes in Computer Science, vol 1734. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10704208_29
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DOI: https://doi.org/10.1007/10704208_29
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