Abstract
In this paper we present the development of two finished projects that have given us enough knowledge to begin with the implementation of a middleware application based on the MPI extension. This ongoing project is also presented in this document. This middleware allow us to dynamically generate a set of domains that fits to the problem to be solved on an heterogeneous cluster. The main goal is to adapt the partitioning to dynamic and unpredictable load changes on the nodes. We want to adapt the architecture to the problem and not the problem to the architecture.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Sander, L., Meakin, P., Ramanlal, P., Ball, R.C.: Ballistic deposition on surfaces. Phys. Rev. A 1, 34 (1986)
Krug, J.: The columnar growth angle in obliquely evaporated thin films. Matterwissen Werkstofft. 26, 22–26 (1995)
Vicsek, T.: Fractal Growth Phenomena. World Scientific, Singapore (1989)
Hara, T.: A stochastic model and the moment dynamics of the growth of amorphous films. J. Theor. Biol. 1, 109 (1984)
Meakin, P., Krug, J., Kassner, K., Family, F.: Laplacian needle growth. Europhys. Lett. 1, 27 (1993)
Krug, J.: Origins if Scale Invariance in Growth Processes. Taylor & Francis, London (1997)
Oliva, A.I., Anguiano, E., Sacedón, J.L., Aguilar, M., Méndez, J.A., Aznérez, J.A.: Extended statistical analysis of rough growth fronts in gold films prepared by thermal evaporation. Phys. Rev. B 60, 2720–2727 (1999)
Mandelbrot, B.B.: The Fractal Geometry of Nature. Freeman, New York (1982)
Meakin, P.: Fractals, Scaling & Growth Far from Equilibrium. Cambridge University Press, Cambridge (1998)
Family, F., Vicsek, T.: Dynamics of Fractal Surfaces. World Scientific, Singapore (1989)
Mullins, W.W.: Solid Surface Morphologies Governed by Capillarity, Metal Surfaces Structure, Energetics and Kinetics. Gjostein, N.A., Robertson, W.D. (1963)
Michely, T., Krug, J.: Islands, Mounds, and Atoms. Patterns and Processes in Crystal Growth Far from Equilibrium. Springer Series in Surface Sciences, vol. 42. Springer, Berlin (2004)
Castañeda-Marroquín, C., Navarrete, C.B., Ortega, A., Alfonseca, M., Anguiano, E.: Parallel Metropolis-Montecarlo simulation for Potts model using an adaptable network topology based on dynamic graph partitioning. In: ISPDC ’08 (2008)
Andrew, R.S.: Reliability in LAM/MPI
Burns, G., Daoud, R., Vaigl, J.: LAM: An open cluster environment for MPI
Forum, M.P.I.: MPI: A message-passing interface standard. Technical Report UT-CS-94-230 (1994)
Mascagni, M., Chi, H.: Parallel linear congruential generators with Sophie-Germain moduli. Parallel Comput. 30(11), 1217–1231 (2004)
Culler, D.E., Gupta, A., Singh, J.P.: Parallel Computer Architecture: A Hardware/Software Approach. Kaufmann, San Francisco (1997)
Alexander, A., Mark, C., Rejniak, K.A.: Single-Cell-Based Models in Biology and Medicine. Birkhäuser, Basel (2007)
Graner, J.G.F.: Simulation of biological cell sorting using a 2-dimensional extended Potts model. Phys. Rev. Lett. 69(13), 2013–2016 (1992)
Poplawski, N.J., Swat, M., Gens, J.S., Glazier, J.A.: Adhesion between cells, diffusion of growth factors, and elasticity of the aer produce the paddle shape of the chick limb. Phys. A, Stat. Theor. Phys. 373, 521–532 (2007)
Turner, S., Sherratt, J.A.: Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model
Rosenbluth, M., Teller, A., Teller, E., Metropolis, N., Rosenbluth, A.: Equation of state calculations by fast computing machines. J. Chem. Phys. 21(13), 1087–1092 (1953)
Chen, N., Glazier, J.A., Izaguirre, J.A., Alber, M.S.: A parallel implementation of the cellular Potts model for simulation of cell-based morphogenesis. Comput. Phys. Commun. 176(11–12), 670–681 (2007)
Cercato, F.P., Mombach, J.C.M., Cavalheiro, G.G.H.: High performance simulations of the cellular Potts model. In: High Performance Computing Systems and Applications, Annual International Symposium on, 0:28 (2006)
Gusatto, E., Mombach, J.C.M., Cercato, F.P., Cavalheiro, G.H.: An efficient parallel algorithm to evolve simulations of the cellular Potts model. Parallel Process. Lett. 15(12), 199–208 (2005)
Chen, N., Glazier, J.A., Izaguirre, J.A., Alber, M.B.: A parallel implementation of the cellular Potts model for simulation of cell-based morphogenesis. Comput. Phys. Commun. 176(11–12), 670–681 (2007)
Canal, R., Parcerisa, J., Gonzalez, A.: Dynamic cluster assignment mechanisms. In: HPCA, p. 133 (2000)
Bhargava, R., John, L.: Improving dynamic cluster assignment for clustered trace cache processors. Technical report (2003)
Amiri, K., Petrou, D., Ganger, G., Gibson, G.: Dynamic function placement in active storage clusters. Technical report (1999)
Lastovetsky, A.: Scientific programming for heterogene us systems—bridging the gap between algorithms and applications. In: PARELEC’06 IEEE Proceedings, pp. 3–8 (2006)
von Hanxleden, R., Scott, L.R.: Load balancing on message passing architectures. J. Parallel Distrib. Comput. 13(3), 312–324 (1991)
Nicol, D.M., Saltz, J.H.: Dynamic remapping of parallel computations with varying resource demands. IEEE Trans. Comput. 37(9), 1073–1087 (1988)
Kumar, S., Das, S.K., Biswas, R.: Graph partitioning for parallel applications in heterogeneous grid environments. In: IPDPS ’02: Proceedings of the 16th International Symposium on Parallel and Distributed Processing, p. 66 (2002)
Bacigalupo, D.A., Jarvis, S.A., He, L., Spooner, D.P., Nudd, G.R.: Comparing layered queuing and historical performance models of a distributed enterprise application. In: IASTED International Conference on Parallel and Distributed Computing and Networks, pp. 608–613 (2005)
Bacigalupo, D.A., Jarvis, S.A., He, L., Spooner, D., Pelych, D., Nudd, G.R.: A comparative evaluation of two techniques for predicting the performance of dynamic enterprise systems. In: PARCO, pp. 163–170 (2005)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Navarrete, C.B., Anguiano, E. (2010). From Static Domains to Graph Decomposition for Heterogeneous Cluster Programming. In: Resch, M., Roller, S., Benkert, K., Galle, M., Bez, W., Kobayashi, H. (eds) High Performance Computing on Vector Systems 2009. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03913-3_11
Download citation
DOI: https://doi.org/10.1007/978-3-642-03913-3_11
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-03912-6
Online ISBN: 978-3-642-03913-3
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)