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

Shaahin Angizi1,a, Jiao Sun2, Wei Zhang2,b and Deliang Fan3
1Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL
aangizi@knights.ucf.edu
2Department of Computer Science, University of Central Florida, Orlando, FL
bwzhang.cs@ucf.edu
3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ
dfan@asu.edu

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 FMindex 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.



Full Text (PDF)