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Efficiency of Various Tiling Strategies for the Zuker Algorithm Optimization

Author

Listed:
  • Piotr Blaszynski

    (Faculty of Computer Science and Information Systems, West Pomeranian University of Technology, Zolnierska 49, 72210 Szczecin, Poland
    These authors contributed equally to this work.)

  • Marek Palkowski

    (Faculty of Computer Science and Information Systems, West Pomeranian University of Technology, Zolnierska 49, 72210 Szczecin, Poland
    These authors contributed equally to this work.)

  • Wlodzimierz Bielecki

    (Faculty of Computer Science and Information Systems, West Pomeranian University of Technology, Zolnierska 49, 72210 Szczecin, Poland
    These authors contributed equally to this work.)

  • Maciej Poliwoda

    (Faculty of Computer Science and Information Systems, West Pomeranian University of Technology, Zolnierska 49, 72210 Szczecin, Poland
    These authors contributed equally to this work.)

Abstract

This paper focuses on optimizing the Zuker RNA folding algorithm, a bioinformatics task with non-serial polyadic dynamic programming and non-uniform loop dependencies. The intricate dependence pattern is represented using affine formulas, enabling the automatic application of tiling strategies via the polyhedral method. Three source-to-source compilers—PLUTO, TRACO, and DAPT—are employed, utilizing techniques such as affine transformations, the transitive closure of dependence relation graphs, and space–time tiling to generate cache-efficient codes, respectively. A dedicated transpose code technique for non-serial polyadic dynamic programming codes is also examined. The study evaluates the performance of these optimized codes for speed-up and scalability on multi-core machines and explores energy efficiency using RAPL. The paper provides insights into related approaches and outlines future research directions within the context of bioinformatics algorithm optimization.

Suggested Citation

  • Piotr Blaszynski & Marek Palkowski & Wlodzimierz Bielecki & Maciej Poliwoda, 2024. "Efficiency of Various Tiling Strategies for the Zuker Algorithm Optimization," Mathematics, MDPI, vol. 12(5), pages 1-13, February.
    • Handle: RePEc:gam:jmathe:v:12:y:2024:i:5:p:728-:d:1348695
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