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Detecting Secondary Bottlenecks In Parallel Quantum Chemistry Applications Using Mpi

Author

Listed:
  • REEMA MAHAJAN

    (Department of Chemical Engineering, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi-16, India)

  • DIETER KRANZLMÜLLER

    (Institute of Graphics and Parallel Processing, Johannes Kepler University Linz, Altenberger Straße 69, A-4040, Linz, Austria)

  • JENS VOLKERT

    (Institute of Graphics and Parallel Processing, Johannes Kepler University Linz, Altenberger Straße 69, A-4040, Linz, Austria)

  • ULRICH H. E. HANSMANN

    (Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49331-1295, USA;
    John v. Neumann Institute for Computing, Forschungszentrum Jülich, 52425 Jülich, Germany)

  • SIEGFRIED HÖFINGER

    (Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49331-1295, USA)

Abstract

Profiling tools such asgprofandssrunare used to analyze the run-time performance of a scientific application. The profiling is done in serial and in parallel mode using MPI as the communication interface. The application is a quantum chemistry program using Hartree Fock theory and Pulays DIIS method. An extensive set of test cases is taken into account in order to reach uniform conclusions. A known problem with decreased parallel scalability can thus be narrowed down to a single subroutine responsible for the reduction in Speed Up. The critical module is analyzed and a typical pitfall with triple matrix multiplications is identified. After overhauling the critical subroutine re-examination of the run-time behavior shows significantly improved performance and markedly improved parallel scalability. The lessons learned here might be of interest to other people working in similar fields with similar problems.

Suggested Citation

  • Reema Mahajan & Dieter Kranzlmüller & Jens Volkert & Ulrich H. E. Hansmann & Siegfried Höfinger, 2008. "Detecting Secondary Bottlenecks In Parallel Quantum Chemistry Applications Using Mpi," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 19(01), pages 1-13.
    • Handle: RePEc:wsi:ijmpcx:v:19:y:2008:i:01:n:s0129183108011899
    DOI: 10.1142/S0129183108011899
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