Abstract
In the present work we describe architectural concepts of the distributed molecular simulation package GridMD. The main purpose of this work is to underline the construction patterns which may help to generalize the design of an application for extensive atomistic simulations. The issues such as design-time parallel execution implication, flexibility and extensions, portability to Grid environments and maximal adaptation of existing third-party codes and resources are addressed. The library is being currently developed, with gradually growing number of available components and tools. The basic GridMD engine is a free software and is distributed under the terms of wxWidgets library license [1].
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Kuksin, A.Y., Morozov, I.V., Norman, G.E., Stegailov, V.V., Valuev, I.A.: To appear in Molecular Simulation (2005).
Charm++, http://charm.cs.uiuc.edu/
GAMESS grid portal, https://gridport.npaci.edu/gamess/
Amisaki, T., Fujiwara, S.-I.: Proceedings of the 2004 Symposium on Applications and the Internet-Workshops, p. 614 (2004)
Pytlinski, J., Skorwider, L., Benedyczak, K., Wronski, M., Bala, P., Huber, V., Sloot, P.M.A., et al. (eds.) ICCS 2003. LNCS, vol. 2658, pp. 307–315. Springer, Heidelberg (2003)
Li, Y., Mascagni, M.: Grid-based Monte Carlo Application. In: Parashar, M. (ed.) GRID 2002. LNCS, vol. 2536, pp. 13–25. Springer, Heidelberg (2002)
GridMD development website, http://biolab1.mipt.ru/gridmd
Valuev, I.: Comput. Phys. Comm. 169, 60–63 (2005)
Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design Patterns. Elements of Reusable Object-Oriented Software. Addison Wesley Longman, Amsterdam (1995)
NIMROD website: http://www.csse.monash.edu.au/~davida/nimrod/
Sudholt, W., Baldridge, K., Abramson, D., Enticott, C., Garic, S.: New Generation Computing 22, 125–135 (2004)
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Valuev, I. (2005). GridMD: Program Architecture for Distributed Molecular Simulation. In: Hobbs, M., Goscinski, A.M., Zhou, W. (eds) Distributed and Parallel Computing. ICA3PP 2005. Lecture Notes in Computer Science, vol 3719. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11564621_35
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DOI: https://doi.org/10.1007/11564621_35
Publisher Name: Springer, Berlin, Heidelberg
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