Print Email Facebook Twitter SALoBa Title SALoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs Author Park, Seongyeon (Yonsei University) Kim, Hajin (Yonsei University) Ahmad, T. (TU Delft Computer Engineering) Ahmed, N. (TU Delft Numerical Analysis) Al-Ars, Z. (TU Delft Computer Engineering) Hofstee, H.P. (TU Delft Computer Engineering; IBM) Kim, Youngsok (Yonsei University) Lee, Jinho (Yonsei University) Contributor O'Conner, L. (editor) Date 2022 Abstract Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit exploiting the full computational capability of modern GPUs. This paper presents SALoBa, a GPU-accelerated sequence alignment library focused on seed extension. Based on the analysis of previous work with real-world sequencing data, we propose techniques to exploit the data locality and improve work-load balancing. The experimental results reveal that SALoBa significantly improves the seed extension kernel compared to state-of-the-art GPU-based methods. Subject Genome sequencingSequence alignmentSmith-WatermanGPU acceleration To reference this document use: http://resolver.tudelft.nl/uuid:2e8b2274-eef4-4c79-b76e-76fbfc21c133 DOI https://doi.org/10.1109/IPDPS53621.2022.00076 Publisher IEEE, Piscataway Embargo date 2023-07-01 ISBN 978-1-6654-8107-6 Source Proceedings of the 2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS) Event 2022 IEEE 36th International Parallel and Distributed Processing Symposium, 2022-05-30 → 2022-06-03, Vitual at Lyon, France Bibliographical note Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public. Part of collection Institutional Repository Document type conference paper Rights © 2022 Seongyeon Park, Hajin Kim, T. Ahmad, N. Ahmed, Z. Al-Ars, H.P. Hofstee, Youngsok Kim, Jinho Lee Files PDF SALoBa_Maximizing_Data_Lo ... n_GPUs.pdf 940.42 KB Close viewer /islandora/object/uuid:2e8b2274-eef4-4c79-b76e-76fbfc21c133/datastream/OBJ/view