skip to main content
10.1145/2063384.2063469acmconferencesArticle/Chapter ViewAbstractPublication PagesscConference Proceedingsconference-collections
research-article

A scalable eigensolver for large scale-free graphs using 2D graph partitioning

Authors Info & Claims
Published:12 November 2011Publication History

ABSTRACT

Eigensolvers are important tools for analyzing and mining useful information from scale-free graphs. Such graphs are used in many applications and can be extremely large. Unfortunately, existing parallel eigensolvers do not scale well for these graphs due to the high communication overhead in the parallel matrix-vector multiplication (MatVec). We develop a MatVec algorithm based on 2D edge partitioning that significantly reduces the communication costs and embed it into a popular eigensolver library. We demonstrate that the enhanced eigensolver can attain two orders of magnitude performance improvement compared to the original on a state-of-art massively parallel machine. We illustrate the performance of the embedded MatVec by computing eigenvalues of a scale-free graph with 300 million vertices and 5 billion edges, the largest scale-free graph analyzed by any in-memory parallel eigensolver, to the best of our knowledge.

References

  1. A. Abou-rjeili and G. Karypis. Multilevel algorithms for partitioning power-law graphs. In Proceedings, IEEE International Parallel & Distributed Processing Symposium (IPDPS), pages 16--575, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  2. L. Backstrom, D. Huttenlocher, J. Kleinberg, and X. Lan. Group formation in large social networks: membership, growth, and evolution. In Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining, KDD '06, pages 44--54, New York, NY, USA, 2006. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  3. C. G. Baker, U. L. Hetmaniuk, R. B. Lehoucq, and H. K. Thornquist. Anasazi software for the numerical solution of large-scale eigenvalue problems. ACM Trans. Math. Softw., 36:13:1--13:23, July 2009. Google ScholarGoogle ScholarDigital LibraryDigital Library
  4. A.-L. Barabasi and R. Albert. Emergence of scaling in random networks. Science, 286:509, 1999.Google ScholarGoogle ScholarCross RefCross Ref
  5. S. T. Barnard. Pmrsb: parallel multilevel recursive spectral bisection. In Supercomputing '95: Proceedings of the 1995 ACM/IEEE conference on Supercomputing (CDROM), page 27, New York, NY, USA, 1995. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  6. R. Bell, A. D. Malony, and S. Shende. Paraprof: A portable, extensible, and scalable tool for parallel performance profile analysis. In Euro-Par'03, pages 17--26, 2003.Google ScholarGoogle ScholarCross RefCross Ref
  7. M. J. Berger and S. H. Bokhari. A partitioning strategy for nonuniform problems on multiprocessors. IEEE Trans. Comput., 36(5):570--580, 1987. Google ScholarGoogle ScholarDigital LibraryDigital Library
  8. P. Boldi and S. Vigna. The WebGraph framework I: Compression techniques. In Proc. of the Thirteenth International World Wide Web Conference (WWW 2004), pages 595--601, Manhattan, USA, 2004. ACM Press. Google ScholarGoogle ScholarDigital LibraryDigital Library
  9. J. Bradley, D. de Jager, W. Knottenbelt, and A. Trifunović. Hypergraph partitioning for faster parallel pagerank computation. In M. Bravetti, L. Kloul, and G. Zavattaro, editors, Formal Techniques for Computer Systems and Business Processes, volume 3670 of Lecture Notes in Computer Science, pages 155--171. Springer Berlin/Heidelberg, 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  10. A. Broder, R. Kumar, F. Maghoul, P. Raghavan, S. Rajagopalan, R. Stata, and A. Tomkins. Graph structure in the web: Experiments and models. In 9th World Wide Web Conference, 2000. Google ScholarGoogle ScholarDigital LibraryDigital Library
  11. H. Brunst, H.-C. Hoppe, W. E. Nagel, and M. Winkler. Performance optimization for large scale computing: the scalable VAMPIR approach. In ICCS '01: Proceedings of the International Conference on Computational Science-Part II, pages 751--760, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  12. T. N. Bui and C. Jones. A heuristic for reducing fill-in in sparse matrix factorization. In PPSC, pages 445--452, 1993.Google ScholarGoogle Scholar
  13. U. Catalyurek and C. Aykanat. A fine-grain hypergraph model for 2d decomposition of sparse matrices. In Proceedings of the 15th International Parallel & Distributed Processing Symposium, IPDPS '01, pages 118--, Washington, DC, USA, 2001. IEEE Computer Society. Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. U. Catalyurek and C. Aykanat. A hypergraph-partitioning approach for coarse-grain decomposition. In Proceedings of the 2001 ACM/IEEE conference on Supercomputing (CDROM), Supercomputing '01, pages 28--28, New York, NY, USA, 2001. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  15. U. V. Çatalyürek and C. Aykanat. Hypergraph-partitioning based decomposition for parallel sparse-matrix vector multiplication. IEEE Trans. on Parallel and Distributed Systems, 10(7):673--693, 1999. Google ScholarGoogle ScholarDigital LibraryDigital Library
  16. D. Chakrabarti, Y. Zhan, and C. Faloutsos. R-mat: A recursive model for graph mining. In In SDM, 2004.Google ScholarGoogle ScholarCross RefCross Ref
  17. J. Cho, H. Garcia-Molina, T. Haveliwala, W. Lam, A. Paepcke, S. Raghavan, and G. Wesley. Stanford webbase components and applications. ACM Trans. Internet Technol., 6:153--186, May 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  18. A. Clauset, M. E. J. Newman, and C. Moore. Finding community structure in very large networks. Phys. Rev. E, 70(6):066111, Dec. 2004.Google ScholarGoogle ScholarCross RefCross Ref
  19. R. Cooley, B. Mobasher, and J. Srivastava. Web mining: Information and pattern discovery on the world wide web. Tools with Artificial Intelligence, IEEE International Conference on, 0:0558, 1997. Google ScholarGoogle ScholarDigital LibraryDigital Library
  20. J. Duch and A. Arenas. Community detection in complex networks using extremal optimization. Physical Review E, 72:027104, Jan. 2005.Google ScholarGoogle ScholarCross RefCross Ref
  21. S. Dutt. New faster kernighan-lin-type graph-partitioning algorithms. In ICCAD '93: Proceedings of the 1993 IEEE/ACM international conference on Computer-aided design, pages 370--377, Los Alamitos, CA, USA, 1993. IEEE Computer Society Press. Google ScholarGoogle ScholarDigital LibraryDigital Library
  22. C. Farhat and M. Lesoinne. Automatic partitioning of unstructured meshes for the parallel solution of problems in computational mechanics. Internat. J. Numer. Meth. Engrg, 36(5):745--764, 1993.Google ScholarGoogle ScholarCross RefCross Ref
  23. C. M. Fiduccia and R. M. Mattheyses. A linear-time heuristic for improving network partitions. In 25 years of DAC: Papers on Twenty-five years of electronic design automation, pages 241--247, New York, NY, USA, 1988. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. G. Fox et al. Solving Problems on Concurrent Processors. Prentice-Hall, 1988. Google ScholarGoogle ScholarDigital LibraryDigital Library
  25. J. R. Gilbert and E. Zmijewski. A parallel graph partitioning algorithm for a message-passing multiprocessor. Int. J. Parallel Program., 16(6):427--449, 1987. Google ScholarGoogle ScholarDigital LibraryDigital Library
  26. D. Gleich, L. Zhukov, and P. Berkhin. Fast parallel pagerank: A linear system approach. Technical report, Institute for Computation and Mathematical Enginneering, Stanford University, 2004.Google ScholarGoogle Scholar
  27. A. Grama, V. Kumar, and A. Sameh. Parallel matrix-vector product using approximate hierarchical methods. In In Proceedings of Supercomputing '95, 1995. Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. C. Groër, B. D. Sullivan, and S. Poole. A mathematical analysis of the R-MAT random graph generator. Networks, 2011. Google ScholarGoogle ScholarDigital LibraryDigital Library
  29. B. Hendrickson and T. G. Kolda. Graph partitioning models for parallel computing. Parallel Computing, 26:1519--1534, 1999. Google ScholarGoogle ScholarDigital LibraryDigital Library
  30. B. Hendrickson and R. Leland. The Chaco User's Guide, version 2.0. Technical Report SAND95--2344, Sandia National Laboratories, 1995.Google ScholarGoogle Scholar
  31. B. Hendrickson and R. Leland. A multilevel algorithm for partitioning graphs. In Supercomputing '95: Proceedings of the 1995 ACM/IEEE conference on Supercomputing (CDROM), page 28, New York, NY, USA, 1995. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  32. B. Hendrickson, R. Leland, and S. Plimpton. An efficient parallel algorithm for matrix-vector multiplication. Int. Journal of High Speed Computing, 7(1):73--88, 1995.Google ScholarGoogle ScholarCross RefCross Ref
  33. V. Hernandez, J. E. Roman, and V. Vidal. Slepc: A scalable and flexible toolkit for the solution of eigenvalue problems. ACM Trans. Math. Softw., 31(3):351--362, 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  34. Hyperion. https://hyperionproject.llnl.gov.Google ScholarGoogle Scholar
  35. IBM Blue Gene/P. www-03.ibm.com/systems/deepcomputing/solutions/bluegene.Google ScholarGoogle Scholar
  36. Y. Ji, X. Xu, and G. D. Stormo. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics, 20(10):1603--1611, 2004. Google ScholarGoogle ScholarDigital LibraryDigital Library
  37. M. Jones and P. Plassman. Computational results for parallel unstructured mesh computations. Technical Report UT-CS-94-248, Computer Science Department, University of Tennesse, 1994. Google ScholarGoogle ScholarDigital LibraryDigital Library
  38. G. Karypis and V. Kumar. A fast and high quality multilevel scheme for partitioning irregular graphs. Technical Report 95--035, University of Minnesota, Dept. of Computer Science, 1995.Google ScholarGoogle Scholar
  39. G. Karypis and V. Kumar. MeTis: Unstrctured Graph Partitioning and Sparse Matrix Ordering System, Version 2.0, 1995.Google ScholarGoogle Scholar
  40. G. Karypis and V. Kumar. Multilevel k-way partitioning scheme for irregular graphs. Technical Report 95--064, University of Minnesota, Dept. of Computer Science, 1995.Google ScholarGoogle Scholar
  41. G. Karypis and V. Kumar. Parallel multilevel k-way partitioning scheme for irregular graphs. In Supercomputing '96: Proceedings of the 1996 ACM/IEEE conference on Supercomputing (CDROM), page 35, Washington, DC, USA, 1996. IEEE Computer Society. Google ScholarGoogle ScholarDigital LibraryDigital Library
  42. G. Karypis and V. Kumar. A coarse-grain parallel formulation of multilevel k-way graph partitioning algorithm. In PPSC, 1997.Google ScholarGoogle Scholar
  43. G. Karypis and V. Kumar. A parallel algorithm for multilevel graph partitioning and sparse matrix ordering. J. Parallel Distrib. Comput., 48(1):71--95, 1998. Google ScholarGoogle ScholarDigital LibraryDigital Library
  44. B. Kernighan and S. Lin. An efficient heuristics for partitioning graphs. Technical report, The Bell System Technical Journal, 1970.Google ScholarGoogle Scholar
  45. R. Kosala and H. Blockeel. Web mining research: a survey. SIGKDD Explor. Newsl., 2:1--15, June 2000. Google ScholarGoogle ScholarDigital LibraryDigital Library
  46. R. Leland and B. Hendrickson. An emperical study of static load balancing algorithms. In Scalable High-Performance Comput. Conf., pages 682--685, 1994.Google ScholarGoogle Scholar
  47. J. G. Lewis and R. A. van de Geijn. Distributed memory matrix-vector multiplication and conjugate gradient algorithms. In IEEE, editor, Proceedings, Supercomputing '93: Portland, Oregon, November 15--19, 1993, pages 484--492, pub-IEEE:adr, 1993. IEEE Computer Society Press. Google ScholarGoogle ScholarDigital LibraryDigital Library
  48. D. Liben-Nowell and J. Kleinberg. The link-prediction problem for social networks. J. Am. Soc. Inf. Sci. Technol., 58:1019--1031, May 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  49. K. Maschhoff and D. Sorensen. P_ARPACK: An efficient portable large scale eigenvalue package for distributed memory parallel architectures. In J. Wasniewski, J. Dongarra, K. Madsen, and D. Olesen, editors, Applied Parallel Computing Industrial Computation and Optimization, volume 1184 of Lecture Notes in Computer Science, pages 478--486. Springer Berlin/Heidelberg, 1996. Google ScholarGoogle ScholarDigital LibraryDigital Library
  50. E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. In ISMB (Supplement of Bioinformatics), pages 302--310, 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  51. M. E. J. Newman. Detecting community structure in networks. European Physical Journal B, 38:321--330, May 2004.Google ScholarGoogle ScholarCross RefCross Ref
  52. M. E. J. Newman. Fast algorithm for detecting community structure in networks. Phys. Rev. E, 69(6):066133, June 2004.Google ScholarGoogle ScholarCross RefCross Ref
  53. M. E. J. Newman and M. Girvan. Finding and evaluating community structure in networks. Phys. Rev. E, 69(2):026113, Feb. 2004.Google ScholarGoogle ScholarCross RefCross Ref
  54. F. Pellegrini. Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. http://www.labri.fr/perso/pelegrin/scotch/.Google ScholarGoogle Scholar
  55. A. Pinar and M. T. Heath. Improving performance of sparse matrix-vector multiplication. In Proceedings of the 1999 ACM/IEEE conference on Supercomputing (CDROM), Supercomputing '99, 1999. Google ScholarGoogle ScholarDigital LibraryDigital Library
  56. Portable, Extensible Toolkit for Scientific Computation. http://www.mcs.anl.gov/petsc/petsc-as.Google ScholarGoogle Scholar
  57. A. Pothen, H. D. Simon, and K.-P. Liou. Partitioning sparse matrices with eigenvectors of graphs. SIAM J. Matrix Anal. Appl., 11(3):430--452, 1990. Google ScholarGoogle ScholarDigital LibraryDigital Library
  58. Y. Saad. Iterative Methods for Sparse Linear Systems. Society for Industrial and Applied Mathematics, 2nd edition, 2003. Google ScholarGoogle ScholarDigital LibraryDigital Library
  59. A. Schenker. Graph-theoretic techniques for web content mining. PhD thesis, Tampa, FL, USA, 2003. AAI3182715. Google ScholarGoogle ScholarDigital LibraryDigital Library
  60. J. Scott. Social Network Analysis: A Handbook. SAGE Publications, London, UK, 1991.Google ScholarGoogle Scholar
  61. H. D. Simon. Partitioning of unstructured problems for parallel processing. Computing Systems in Engineering, 2:135--148, 1991.Google ScholarGoogle ScholarCross RefCross Ref
  62. A. Stathopoulos and J. R. McCombs. PRIMME: PReconditioned Iterative MultiMethod Eigensolver: Methods and software description. ACM Trans. Math. Software, 37(2):21:1--21:30, 2010. Google ScholarGoogle ScholarDigital LibraryDigital Library
  63. The Graph500. http://www.graph500.org.Google ScholarGoogle Scholar
  64. B. Vastenhouw and R. H. Bisseling. A two-dimensional data distribution method for parallel sparse matrix-vector multiplication. SIAM Rev., 47:67--95, January 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  65. S. Wasserman and K. Faust. Social network analysis: methods and applications. Cambridge University Press, 1994.Google ScholarGoogle ScholarCross RefCross Ref
  66. S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, and J. Demmel. Optimization of sparse matrix-vector multiplication on emerging multicore platforms. Parallel Computing, 35(3):178--194, 2009. Google ScholarGoogle ScholarDigital LibraryDigital Library
  67. A. Yoo, E. Chow, K. Henderson, W. McLendon, B. Hendrickson, and Ümit Çatalyürek. A scalable distributed parallel breadth-first search algorithm on bluegene/l. In Proceedings of Supercomputing'05, Nov. 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  68. A. Yoo and K. Henderson. Parallel massive scale-free graph generators, 2010. http://arxiv.org/pdf/1003.3684v1.Google ScholarGoogle Scholar
  69. Z. Zohan, K. Mathur, S. Johnson, and T. Hughes. An efficient communication strategy for finite element methods on the connection machine cm-5 system. Technical Report TR-11-93, Parallel Computing Research Group, Center for Research in Computing Technology, Harvard University, 1993.Google ScholarGoogle Scholar
  70. Z. Zohan, K. Mathur, S. Johnson, and T. Hughes. Parallel implementation of recursive spectral bisection on the connection machine cm-5 system. Technical Report TR-07-94, Parallel Computing Research Group, Center for Research in Computing Technology, Harvard University, 1994.Google ScholarGoogle Scholar

Index Terms

  1. A scalable eigensolver for large scale-free graphs using 2D graph partitioning

        Recommendations

        Comments

        Login options

        Check if you have access through your login credentials or your institution to get full access on this article.

        Sign in
        • Published in

          cover image ACM Conferences
          SC '11: Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
          November 2011
          866 pages
          ISBN:9781450307710
          DOI:10.1145/2063384

          Copyright © 2011 ACM

          Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

          Publisher

          Association for Computing Machinery

          New York, NY, United States

          Publication History

          • Published: 12 November 2011

          Permissions

          Request permissions about this article.

          Request Permissions

          Check for updates

          Qualifiers

          • research-article

          Acceptance Rates

          SC '11 Paper Acceptance Rate74of352submissions,21%Overall Acceptance Rate1,516of6,373submissions,24%

        PDF Format

        View or Download as a PDF file.

        PDF

        eReader

        View online with eReader.

        eReader