This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Accelerating Pairwise Computations on Cell Processors
January 2011 (vol. 22 no. 1)
pp. 69-77
Abhinav Sarje, Iowa State University, Ames
Jaroslaw Zola, Iowa State University, Ames
Srinivas Aluru, Iowa State University, Ames and Indian Institute of Technology Bombay, Mumbai
Direct computation of all pairwise distances or interactions is a fundamental problem that arises in many application areas including particle or atomistic simulations, fluid dynamics, computational electromagnetics, materials science, genomics and systems biology, and clustering and data mining. In this paper, we present methods for performing such pairwise computations efficiently in parallel on Cell processors. This problem is particularly challenging on the Cell processor due to the small sized Local Stores of the Synergistic Processing Elements, the main computational cores of the processor. We present techniques for different variants of this problem including those with large number of entities or when the dimensionality of the information per entity is large. We demonstrate our methods in the context of multiple applications drawn from fluid dynamics, materials science and systems biology, and present detailed experimental results. Our software library is an open source and can be readily used by application scientists to accelerate pairwise computations using Cell accelerators.

[1] B. Hendrickson and S. Plimpton, "Parallel Many-Body Simulations without All-to-All Communication," J. Parallel and Distributed Computing, vol. 27, pp. 15-25, 1995.
[2] B. Hariharan, S. Aluru, and B. Shanker, "A Scalable Parallel Fast Multipole Method for Analysis of Scattering from Perfect Electrically Conducting Surfaces," Proc. ACM/IEEE Conf. Supercomputing, pp. 1-17, 2002.
[3] P. Hanrahan, D. Salzman, and L. Aupperle, "A Rapid Hierarchical Radiosity Algorithm," Proc. ACM SIGGRAPH '91, pp. 197-206, 1991.
[4] J. Zola, A. Sarje, and S. Aluru, "Constructing Gene Regulatory Networks on Clusters of Cell Processors," Proc. Int'l Conf. Parallel Processing (ICPP '09), pp. 108-115, 2009.
[5] P. Berkhin,"A Survey of Clustering Data Mining Techniques," Grouping Multidimensional Data, pp. 25-71, Springer, 2006.
[6] M. Vikram, A. Baczewzki, B. Shanker, and S. Aluru, "Parallel Accelerated Cartesian Expansions for Particle Dynamics Simulations," Proc. 24th IEEE Int'l Parallel and Distributed Processing Symp. (IPDPS '09), pp. 1-11, 2009.
[7] N. Arora, A. Shringarpure, and R. Vuduc, "Direct N-Body Kernels for Multicore Platforms," Proc. Int'l Conf. Parallel Processing (ICPP '09), pp. 379-387, 2009.
[8] A. Wirawan, B. Schmidt, and C.K. Kwoh, "Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine," Proc. Ninth Int'l Conf. Computational Science (ICCS '09), pp. 954-963, 2009.
[9] K.J. Barker et al., "Entering the Petaflop Era: The Architecture and Performance of Roadrunner," Proc. ACM/IEEE Conf. Supercomputing, pp. 1-11, 2008.
[10] J.A. Kahle et al., "Introduction to the Cell Multiprocessor," IBM J. Research and Development, vol. 49, nos. 4/5, pp. 589-604, 2005.
[11] T. Chen, R. Raghavan, J.N. Dale, and E. Iwata, "Cell Broadband Engine Architecture and Its First Implementation: A Performance View," IBM J. Research and Development, vol. 51, no. 5, pp. 559-572, 2007.
[12] B. Ganapathysubramanian and N. Zabaras, "A Non-Linear Dimension Reduction Methodology for Generating Data-Driven Stochastic Input Models," J. Computational Physics, vol. 227, pp. 6612-6637, 2008.
[13] J.C. Caruso and N. Cliff, "Empirical Size, Coverage, and Power of Confidence Intervals for Spearman's Rho," Educational and Psychological Measurement, vol. 57, pp. 637-654, 1997.
[14] C.O. Daub, R. Steuer, J. Selbig, and S. Kloska, "Estimating Mutual Information Using B-Spline Functions —An Improved Similarity Measure for Analysing Gene Expression Data," BMC Bioinformatics, vol. 5, no. 118, 2004.
[15] Y. Moon, B. Rajagopalan, and U. Lall, "Estimation of Mutual Information Using Kernel Density Estimators," Physical Rev. E, vol. 52, no. 3 pp. 2318-2321, 1995.
[16] K.D. Jones, T.C. Lund, and M.F. Platzer, Experimental and Computational Investigation of Flapping-Wing Propulsion for Micro Air Vehicles, vol. 195, pp. 307-339, AIAA, 2001.
[17] Z.J. Wang, "Vortex Shedding and Frequency Selection in Flapping Flight," J. Fluid Mechanics, vol. 410, pp. 323-341, 2000.
[18] B. Ganapathysubramanian and N. Zabaras, "Modelling Diffusion in Random Heterogeneous Media: Data-Driven Models, Stochastic Collocation and the Variational Multi-Scale Method," J. Computational Physics, vol. 226, pp. 326-353, 2007.
[19] "Cell Broadband Engine Resource Center," http://www.ibm. com/developerworks/power cell/, 2009.
[20] T.M. Cover and J.A. Thomas, Elements of Information Theory, second ed. Wiley, 2006.
[21] I. Priness, O. Maimon, and I. Ben-Gal, "Evaluation of Gene-Expression Clustering via Mutual Information Distance Measure," BMC Bioinformatics, vol. 8, p. 111, 2007.
[22] I. Ulitsky and R. Shamir, "Identification of Functional Modules Using Network Topology and High-Throughput Data," BMC Systems Biology, vol. 1, p. 8, 2007.
[23] A. Kraskov and P. Grassberger,"MIC Mutual Information Based Hierarchical Clustering," Information Theory and Statistical Learning, pp. 101-123, Springer, 2009.
[24] K. Basso et al., "Reverse Engineering of Regulatory Networks in Human B Cells," Nature Genetics, vol. 37, no. 4, pp. 382-390, 2005.
[25] J. Zola, M. Aluru, and S. Aluru, "Parallel Information Theory Based Construction of Gene Regulatory Networks," Proc. 15th Ann. IEEE Int'l Conf. High Performance Computing (HiPC '08), pp. 336-349, 2008.
[26] J.J. Faith et al., "Large-Scale Mapping and Validation of Escherichia Coli Transcriptional Regulation from a Compendium of Expression Profiles," PLoS Biology, vol. 5, no. 1, p. e8, 2007.
[27] S. Khan et al., "Relative Performance of Mutual Information Estimation Methods for Quantifying the Dependence among Short and Noisy Data," Physical Rev. E, vol. 76, p. 026209, 2007.

Index Terms:
Parallel algorithms, computations on matrices, cell broadband engine, pairwise computations, heterogeneous (hybrid) systems, multicore/single-chip multiprocessors.
Citation:
Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru, "Accelerating Pairwise Computations on Cell Processors," IEEE Transactions on Parallel and Distributed Systems, vol. 22, no. 1, pp. 69-77, Jan. 2011, doi:10.1109/TPDS.2010.65
Usage of this product signifies your acceptance of the Terms of Use.