research-article

Exploring DNA Alignment-in-Memory Leveraging Emerging SOT-MRAM

Authors:

Shaahin Angizi,

Deliang FanAuthors Info & Claims

GLSVLSI '20: Proceedings of the 2020 on Great Lakes Symposium on VLSI

Pages 277 - 282

https://doi.org/10.1145/3386263.3407590

Published: 07 September 2020 Publication History

Abstract

In this work, we review two alternative Processing-in-Memory (PIM) accelerators based on Spin-Orbit-Torque Magnetic Random Access Memory (SOT-MRAM) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first discuss the reconstruction of the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented leveraging PIM functions. We then transform SOT-MRAM array to a potential computational memory by presenting two different reconfigurable sense amplifiers to accelerate the reconstructed alignment-in-memory algorithm. The cross-layer simulation results show that such PIM platforms are able to achieve a nearly ten-fold and two-fold increases in throughput/power/area measure compared with recent ASIC and processing-in-ReRAM designs, respectively.

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Cited By

Sahruri AMargala MCilingiroglu U(2024)HiCTL: High Fan-in Differential Capacitive-Threshold-Logic Gate Implementation With an Offset-Compensated Comparator2024 25th International Symposium on Quality Electronic Design (ISQED)10.1109/ISQED60706.2024.10528704(1-7)Online publication date: 3-Apr-2024
https://doi.org/10.1109/ISQED60706.2024.10528704
Zhang FAngizi SSun JZhang WFan D(2023)Aligner-D: Leveraging In-DRAM Computing to Accelerate DNA Short Read AlignmentIEEE Journal on Emerging and Selected Topics in Circuits and Systems10.1109/JETCAS.2023.324154513:1(332-343)Online publication date: Mar-2023
https://doi.org/10.1109/JETCAS.2023.3241545
Mutlu OFirtina C(2023)Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design2023 60th ACM/IEEE Design Automation Conference (DAC)10.1109/DAC56929.2023.10247887(1-4)Online publication date: 9-Jul-2023
https://doi.org/10.1109/DAC56929.2023.10247887
Show More Cited By

Index Terms

Exploring DNA Alignment-in-Memory Leveraging Emerging SOT-MRAM
1. Hardware
  1. Emerging technologies
    1. Analysis and design of emerging devices and systems
  2. Integrated circuits
    1. Semiconductor memory
      1. Non-volatile memory

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cover image ACM Other conferences

GLSVLSI '20: Proceedings of the 2020 on Great Lakes Symposium on VLSI

September 2020

597 pages

ISBN:9781450379441

DOI:10.1145/3386263

General Chairs:
Tinoosh Mohsenin
University of Maryland, Baltimore County, USA
,
Weisheng Zhao
Beihang University, China
,
Program Chairs:
Yiran Chen
Duke University, USA
,
Onur Mutlu
ETH Zurich, Switzerland

Copyright © 2020 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 07 September 2020

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GLSVLSI '20

GLSVLSI '20: Great Lakes Symposium on VLSI 2020

September 7 - 9, 2020

Virtual Event, China

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Cited By

Sahruri AMargala MCilingiroglu U(2024)HiCTL: High Fan-in Differential Capacitive-Threshold-Logic Gate Implementation With an Offset-Compensated Comparator2024 25th International Symposium on Quality Electronic Design (ISQED)10.1109/ISQED60706.2024.10528704(1-7)Online publication date: 3-Apr-2024
https://doi.org/10.1109/ISQED60706.2024.10528704
Zhang FAngizi SSun JZhang WFan D(2023)Aligner-D: Leveraging In-DRAM Computing to Accelerate DNA Short Read AlignmentIEEE Journal on Emerging and Selected Topics in Circuits and Systems10.1109/JETCAS.2023.324154513:1(332-343)Online publication date: Mar-2023
https://doi.org/10.1109/JETCAS.2023.3241545
Mutlu OFirtina C(2023)Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design2023 60th ACM/IEEE Design Automation Conference (DAC)10.1109/DAC56929.2023.10247887(1-4)Online publication date: 9-Jul-2023
https://doi.org/10.1109/DAC56929.2023.10247887
Ferreira JFalcao GGomez-Luna JAlser MOrosa LSadrosadati MKim JOliveira GShahroodi TNori AMutlu O(2022)pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO)10.1109/MICRO56248.2022.00067(900-919)Online publication date: Oct-2022
https://doi.org/10.1109/MICRO56248.2022.00067
Oliveira GBoroumand AGhose SGomez-Luna JMutlu O(2022)Heterogeneous Data-Centric Architectures for Modern Data-Intensive Applications: Case Studies in Machine Learning and Databases2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI)10.1109/ISVLSI54635.2022.00060(273-278)Online publication date: Jul-2022
https://doi.org/10.1109/ISVLSI54635.2022.00060
Garzón EYavits LLanuzza MTeman AWebster J(2022)Emerging Memory Structures for VLSI CircuitsWiley Encyclopedia of Electrical and Electronics Engineering10.1002/047134608X.W8438(1-28)Online publication date: 12-May-2022
https://doi.org/10.1002/047134608X.W8438

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