Work

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

Year: 2024

Type: conference-paper

Abstract: 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.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.15085922

Authors: Mognol, Meven, Lavenier, Dominique, Legriel, Julien

Institutions: Centre National de la Recherche Scientifique, Institut national de recherche en sciences et technologies du numérique, Institut de Recherche en Informatique et Systèmes Aléatoires, Université de Rennes

Language: English

Topic: Parallel Computing and Optimization Techniques

Subfield: Hardware and Architecture

Field: Computer Science

Domain: Physical Sciences

Open Access status: green

Funder: European Commission

Award: G2342797219