SALSA: A domain specific architecture for sequence alignment

Lorenzo Di Tucci, Riyadh Baghdadi, Saman Amarasinghe, Marco D. Santambrogio

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The explosion of genomic data is fostering research in fields such as personalized medicine and agritech, raising the necessity of providing more performant, power-efficient and easy-to-use architectures. Devices such as GPUs and FPGAs, deliver major performance improvements, however, GPUs present no-table power consumption, while FPGAs lack programmability. In this paper, we present SALSA, a Domain-Specific Architecture for sequence alignment that is completely configurable, extensible and is based on the RISC-V ISA. SALSA delivers good performance even at 200 MHz, outperforming Rocket, an open-source core, and an Intel Xeon by factors up to 350x in performance and 790x in power efficiency.

Original languageEnglish (US)
Title of host publicationProceedings - 2020 IEEE 34th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages147-150
Number of pages4
ISBN (Electronic)9781728174457
DOIs
StatePublished - May 2020
Event34th IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2020 - New Orleans, United States
Duration: May 18 2020May 22 2020

Publication series

NameProceedings - 2020 IEEE 34th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2020

Conference

Conference34th IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2020
CountryUnited States
CityNew Orleans
Period5/18/205/22/20

Keywords

  • Domain Specific Architecture
  • Genomics
  • SALSA
  • Sequence Alignment
  • Systolic arrays

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Hardware and Architecture
  • Safety, Risk, Reliability and Quality
  • Control and Optimization

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