PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment

Shaahin Angizi, Jiao Sun, Wei Zhang, Deliang Fan

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

1 Scopus citations

Abstract

In this paper, we propose a high-throughput and energy-efficient Processing-in-Memory accelerator (PIM-Aligner) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first reconstruct the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented in PIM platforms. It supports exact alignment and also handles mismatches to reduce excessive backtracking. We then develop PIM-Aligner platform that transforms SOT-MRAM array to a potential computational memory to accelerate the reconstructed alignment-in-memory algorithm incurring a low cost on top of original SOT-MRAM chips (less than 10% of chip area). Accordingly, we present a local data partitioning, mapping, and pipeline technique to maximize the parallelism in multiple computational sub-array while doing the alignment task. The simulation results show that PIM-Aligner outperforms recent platforms based on dynamic programming with ∼ 3.1× higher throughput per Watt. Besides, PIM-Aligner improves the short read alignment throughput per Watt per mm2 by ∼ 9× and 1.9× compared to FM-index-based ASIC and processing-in-ReRAM designs, respectively.

Original languageEnglish (US)
Title of host publicationProceedings of the 2020 Design, Automation and Test in Europe Conference and Exhibition, DATE 2020
EditorsGiorgio Di Natale, Cristiana Bolchini, Elena-Ioana Vatajelu
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1265-1270
Number of pages6
ISBN (Electronic)9783981926347
DOIs
StatePublished - Mar 2020
Event2020 Design, Automation and Test in Europe Conference and Exhibition, DATE 2020 - Grenoble, France
Duration: Mar 9 2020Mar 13 2020

Publication series

NameProceedings of the 2020 Design, Automation and Test in Europe Conference and Exhibition, DATE 2020

Conference

Conference2020 Design, Automation and Test in Europe Conference and Exhibition, DATE 2020
CountryFrance
CityGrenoble
Period3/9/203/13/20

ASJC Scopus subject areas

  • Hardware and Architecture
  • Safety, Risk, Reliability and Quality
  • Modeling and Simulation
  • Electrical and Electronic Engineering

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