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- Title
Efficiency of Various Tiling Strategies for the Zuker Algorithm Optimization.
- Authors
Blaszynski, Piotr; Palkowski, Marek; Bielecki, Wlodzimierz; Poliwoda, Maciej
- 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.
- Subjects
DYNAMIC programming; AFFINE transformations; COMPILERS (Computer programs); BIOINFORMATICS software; ENERGY consumption; COMPUTATIONAL biology; PLUTO (Dwarf planet)
- Publication
Mathematics (2227-7390), 2024, Vol 12, Issue 5, p728
- ISSN
2227-7390
- Publication type
Article
- DOI
10.3390/math12050728