Skip to main content

Advertisement

SpringerLink
Log in
Menu
Find a journal Publish with us
Search
Cart
Book cover

European Conference on Parallel Processing

Euro-Par 2011: Euro-Par 2011: Parallel Processing Workshops pp 305–314Cite as

  1. Home
  2. Euro-Par 2011: Parallel Processing Workshops
  3. Conference paper
On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections

On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections

  • Hasan Metin Aktulga30,
  • Chao Yang30,
  • Ümit V. Çatalyürek31,
  • Pieter Maris32,
  • James P. Vary32 &
  • …
  • Esmond G. Ng30 
  • Conference paper
  • 1348 Accesses

  • 1 Citations

Part of the Lecture Notes in Computer Science book series (LNTCS,volume 7155)

Abstract

Obtaining highly accurate predictions on properties of light atomic nuclei using the Configuration Interaction (CI) method requires computing the lowest eigenvalues and associated eigenvectors of a large many-body nuclear Hamiltonian, H. One particular approach, the J-scheme, requires the projection of the H matrix into an invariant subspace. Since the matrices can be very large, enormous computing power is needed while significant stresses are put on the memory and I/O sub-systems. By exploiting the inherent localities in the problem and making use of the MPI one-sided communication routines backed by RDMA operations available in the new parallel architectures, we show that it is possible to reduce the I/O overheads drastically for large problems. This is demonstrated in the subspace projection phase of J-scheme calculations on 6Li nucleus, where our new implementation based on one-sided MPI communications outperforms the previous I/O based implementation by almost a factor of 10.

Keywords

  • Invariant Subspace
  • Communication Overhead
  • Diagonal Block
  • Remote Memory
  • Load Imbalance

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Download conference paper PDF

References

  1. Vary, J.P., Maris, P., Ng, E., Yang, C., Sosonkina, M.: Ab initio nuclear structure: The Large sparse matrix eigenvalue problem. J. Phys. Conf. Ser. 180, 012083 (2009)

    CrossRef  Google Scholar 

  2. Maris, P., Shirokov, A.M., Vary, J.P.: Ab initio nuclear structure simulations: The Speculative F-14 nucleus. Phys. Rev. C 81, 021301 (2010)

    CrossRef  Google Scholar 

  3. Maris, P., Vary, J.P., Navratil, P., Ormand, W.E., Nam, H., Dean, D.J.: Origin of the anomalous long lifetime of 14C. Phys. Rev. Lett. 106, 202502 (2011)

    CrossRef  Google Scholar 

  4. Shirokov, A.M., Mazur, A.I., Zaytsev, S.A., Vary, J.P., Weber, T.A.: Nucleon nucleon interaction in the J matrix inverse scattering approach and few nucleon systems. Phys. Rev. C 70, 044005 (2004)

    CrossRef  Google Scholar 

  5. Shirokov, A.M., Mazur, A.I., Vary, J.P., Mazur, E.A.: Inverse scattering J-matrix approach to nucleon-nucleus scattering and the shell model. Phys. Rev. C 79, 014610 (2009)

    CrossRef  Google Scholar 

  6. Aktulga, H.M., Yang, C., Ng, E., Maris, P., Vary, J.P.: Large-scale Parallel null space calculation for nuclear configuration interaction. In: Proc. of HPCS 2011, Istanbul, Turkey, July 4 - 8 (2011)

    Google Scholar 

  7. Gropp, W., Huss-Lederman, S., Lumsdaine, A., Lusk, E., Nitzberg, B., Saphir, W., Snir, M.: MPI – The Complete Reference. The MPI-2 Extensions, vol. 2. MIT Press, Cambridge (1998)

    Google Scholar 

  8. Gropp, W., Thakur, R.: An Evaluation of Implementation Options for MPI One-Sided Communication. In: Di Martino, B., Kranzlmüller, D., Dongarra, J. (eds.) EuroPVM/MPI 2005. LNCS, vol. 3666, pp. 415–424. Springer, Heidelberg (2005)

    CrossRef  Google Scholar 

  9. Çatalyürek, Ü.V., Kaya, K., Uçar, B.: Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds. In: Proc. of HPDC, The Fourth International Workshop on Data Intensive Distributed Computing (DIDC) (June 2011)

    Google Scholar 

  10. Nieplocha, J., Tipparaju, V., Krishnan, M., Panda, D.: High performance remote memory access comunications: The ARMCI approach. International Journal of High Performance Computing and Applications 20(2), 233–253 (2006)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Hasan Metin Aktulga, Chao Yang & Esmond G. Ng

  2. The Ohio State University, Columbus, OH, 43210, USA

    Ümit V. Çatalyürek

  3. Iowa State University, Ames, IA, 50011, USA

    Pieter Maris & James P. Vary

Authors
  1. Hasan Metin Aktulga
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chao Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ümit V. Çatalyürek
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pieter Maris
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. James P. Vary
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Esmond G. Ng
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Scilytics, Koellnerhofgasse 3/15A, 1010, Vienna, Austria

    Michael Alexander

  2. ICAR-CNR, Via P. Castellino, 111, 80131, Napoli, Italy

    Pasqua D’Ambra

  3. University of Amsterdam, 1090, Amsterdam, Netherlands

    Adam Belloum

  4. Innovative Computing Laboratory, The University of Tennessee, USA

    George Bosilca

  5. Department of Experimental Medicine and Clinic, University Magna Græcia, 88100, Catanzaro, Italy

    Mario Cannataro

  6. Computer Science Department, University of Pisa, Italy

    Marco Danelutto

  7. Second University of Naples, Italy

    Beniamino Di Martino

  8. TU München, Boltzmannstr. 3, 85748, Garching, Germany

    Michael Gerndt

  9. Equipe Runtime, INRIA Bordeaux Sud-Ouest, 33405, Talence Cedex, France

    Emmanuel Jeannot & Raymond Namyst & 

  10. Equipe HIEPACS, INRIA Bordeaux Sud-Ouest, 33405, Talence Cedex, France

    Jean Roman

  11. Oak Ridge National Laboratory, Computer Science and Mathematics Division, 37831-6164, Oak Ridge, TN, USA

    Stephen L. Scott

  12. Department of Scientific Computing, University of Vienna, Nordbergstr. 15/3C, 1090, Vienna, Austrial

    Jesper Larsson Traff

  13. Computer Science and Mathematics Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA

    Geoffroy Vallée

  14. Technische Universität München, Germany

    Josef Weidendorfer

Rights and permissions

Reprints and Permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Aktulga, H.M., Yang, C., Çatalyürek, Ü.V., Maris, P., Vary, J.P., Ng, E.G. (2012). On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections. In: Alexander, M., et al. Euro-Par 2011: Parallel Processing Workshops. Euro-Par 2011. Lecture Notes in Computer Science, vol 7155. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29737-3_35

Download citation

  • .RIS
  • .ENW
  • .BIB
  • DOI: https://doi.org/10.1007/978-3-642-29737-3_35

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-29736-6

  • Online ISBN: 978-3-642-29737-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Share this paper

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

Search

Navigation

  • Find a journal
  • Publish with us

Discover content

  • Journals A-Z
  • Books A-Z

Publish with us

  • Publish your research
  • Open access publishing

Products and services

  • Our products
  • Librarians
  • Societies
  • Partners and advertisers

Our imprints

  • Springer
  • Nature Portfolio
  • BMC
  • Palgrave Macmillan
  • Apress
  • Your US state privacy rights
  • Accessibility statement
  • Terms and conditions
  • Privacy policy
  • Help and support

167.114.118.210

Not affiliated

Springer Nature

© 2023 Springer Nature