Abstract
This paper proposes a new fine-grained data distribution operation MPI_Alltoall_specific that allows an element-wise distribution of data elements to specific target processes. This operation can be used to implement irregular data distribution operations that are required, for example, in particle codes. We present different implementation variants for MPI_Alltoall_specific which are based on collective MPI operations, on point-to-point communication operations, or on parallel sorting. The properties of the implementation variants are discussed and performance results with different data sets are presented. For the performance results two high scaling hardware platforms, including a Blue Gene/P system, are used.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Fitch, B.G., Rayshubskiy, A., Eleftheriou, M., Ward, T.J.C., Giampapa, M., Zhestkov, Y., Pitman, M.C., Suits, F., Grossfield, A., Pitera, J., Swope, W., Zhou, R., Feller, S., Germain, R.S.: Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L. In: Alexandrov, V.N., van Albada, G.D., Sloot, P.M.A., Dongarra, J. (eds.) ICCS 2006. LNCS, vol. 3992, pp. 846–854. Springer, Heidelberg (2006)
Liu, W., Wang, C.L., Prasanna, V.: Portable and scalable algorithm for irregular all-to-all communication. J. Parallel Distrib. Comput. 62(10), 1493–1526 (2002)
Almási, G., Heidelberger, P., Archer, C., Martorell, X., Erway, C., Moreira, J., Steinmacher-Burow, B., Zheng, Y.: Optimization of MPI collective communication on BlueGene/L systems. In: Proc. of the 19th annual Int. Conf. on Supercomputing, pp. 253–262. ACM Press, New York (2005)
Pinar, A., Hendrickson, B.: Interprocessor Communication with Limited Memory. IEEE Trans. Parallel Distrib. Syst. 15(7), 606–616 (2004)
Siegel, S.F., Siegel, A.R.: MADRE: The Memory-Aware Data Redistribution Engine. In: Lastovetsky, A., Kechadi, T., Dongarra, J. (eds.) EuroPVM/MPI 2008. LNCS, vol. 5205, pp. 218–226. Springer, Heidelberg (2008)
Höfler, T., Träff, J.L.: Sparse Collective Operations for MPI. In: Proc. of the 23rd Int. Parallel & Distributed Processing Symposium, HIPS Workshop, pp. 1–8 (2009)
Message Passing Interface Forum: MPI: A Message-Passing Interface Standard Version 2.1. (2008)
Bader, D., Helman, D., JáJá, J.: Practical parallel algorithms for personalized communication and integer sorting. J. Exp. Algorithmics 1, Article No. 3 (1996)
Knuth, D.: The Art of Computer Programming, Volume III: Sorting and Searching, 2nd edn. Addison-Wesley, Reading (1998)
Aluru, S., Sevilgen, F.E.: Parallel Domain Decomposition and Load Balancing Using Space-Filling Curves. In: Proc. of the 4th Int. Conf. on High-Performance Computing, pp. 230–235. IEEE, Los Alamitos (1997)
Dachsel, H., Hofmann, M., Rünger, G.: Library Support for Parallel Sorting in Scientific Computations. In: Kermarrec, A.-M., Bougé, L., Priol, T. (eds.) Euro-Par 2007. LNCS, vol. 4641, pp. 695–704. Springer, Heidelberg (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hofmann, M., Rünger, G. (2009). Fine-Grained Data Distribution Operations for Particle Codes. In: Ropo, M., Westerholm, J., Dongarra, J. (eds) Recent Advances in Parallel Virtual Machine and Message Passing Interface. EuroPVM/MPI 2009. Lecture Notes in Computer Science, vol 5759. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03770-2_12
Download citation
DOI: https://doi.org/10.1007/978-3-642-03770-2_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-03769-6
Online ISBN: 978-3-642-03770-2
eBook Packages: Computer ScienceComputer Science (R0)