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Communication Papers of the 18th Conference on Computer Science and Intelligence Systems

Annals of Computer Science and Information Systems, Volume 37

Polyhedral Tiling Strategies for the Zuker Algorithm Optimization

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DOI: http://dx.doi.org/10.15439/2023F7645

Citation: Communication Papers of the 18th Conference on Computer Science and Intelligence Systems, M. Ganzha, L. Maciaszek, M. Paprzycki, D. Ślęzak (eds). ACSIS, Vol. 37, pages 37–41 ()

Full text

Abstract. In this paper, we focus on optimizing the code for computing the Zuker RNA folding algorithm. This bioinformatics task belongs to the class of non-serial polyadic dynamic programming, which involves non-uniform program loop dependencies. However, its dependence pattern can be represented using affine formulas, allowing us to automatically employ tiling strategies based on the polyhedral method. We use three source-to-source compilers Pluto, Traco, and Dapt based on affine transformations, transitive closure of dependence relation graph and space-time tiling, respectively, to automatically generate cache-efficient codes. We evaluate the speed-up and scalability of optimized codes and check their performance applying two multi-core machines. We also discuss related approaches and outline future work in the conclusion of the paper.

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