Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment - Archive ouverte HAL
Communication Dans Un Congrès Année : 2024

Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment

Résumé

Sequence alignment is an ubiquitous task in genomics analysis whose performance can be affected by the memory-wall on a processor-centric architecture. Processing-in-Memory (PiM) architectures provide a memory system with integrated computing capabilities to alleviate this bottleneck. In this paper, we present a long read optimized version of the Needleman and Wunsch (N&W) algorithm based on PiM devices developed by the UPMEM company. Such memories add 128 computing units to a standard 16GB DIMM. On a server equipped with 20 UPMEM PiMs, our N&W implementation outperforms standard alignment tools by an order of magnitude compared to a traditional multicore server. Code available at https://github.com/upmem/usecase_dpu_alignment
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Dates et versions

hal-04739328 , version 1 (16-10-2024)

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  • HAL Id : hal-04739328 , version 1

Citer

Meven Mognol, Dominique Lavenier, Julien Legriel. Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment. ICPP 2024 - International Conference on Parallel Processing, Aug 2024, Gotland, Sweden. pp.1-10. ⟨hal-04739328⟩
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