Print Email Facebook Twitter KrakenOnMem Title KrakenOnMem: A Memristor-Augmented HW/SW Framework for Taxonomic Profiling Author Shahroodi, Taha Zahedi, M.Z. (TU Delft Computer Engineering) Abhairaj Singh, A. (TU Delft Electrical Engineering, Mathematics and Computer Science) Wong, J.S.S.M. (TU Delft Computer Engineering) Hamdioui, S. (TU Delft Quantum & Computer Engineering) Faculty Electrical Engineering, Mathematics and Computer Science Department Quantum & Computer Engineering Date 2022 Abstract State-of-the-art taxonomic profilers that comprise the first step in larger-context metagenomic studies have proven to be computationally intensive, i.e., while accurate, they come at the cost of high latency and energy consumption. Table Lookup operation is a primary bottleneck of today's profilers. In this paper, we first propose TL-PIM, a hardware accelerator based on the processing-in-memory (PIM) paradigm to accelerate Table Lookup. TL-PIM leverages the in-memory compute capability of emerging memory technologies along with intelligent data mapping. Then, we integrate TL-PIM into Kraken2, a state-of-the-art metagenomic profiler, and build an HW/SW co-designed profiler, called KrakenOnMem. Results from a silicon-based prototype of our emerging memory validate the design and required operations on a smaller scale. Our large-scale calibrated simulations show that KrakenOnMem can provide an average of 61.3% speedup compared to original Kraken2 for end-to-end profiling. Additionally, our design improves the energy consumption by orders of magnitude compared to the original Kraken2 while incurring a negligible area overhead. Subject (Hash) table lookupEmerging memoriesIn memory ProcessingKraken2Taxonomic profiling To reference this document use: http://resolver.tudelft.nl/uuid:ae58263f-8732-48dc-91d4-48898852c710 DOI https://doi.org/10.1145/3524059.3532367 Publisher Association for Computing Machinery (ACM) ISBN 9781450392815 Source Proceedings of the 36th ACM International Conference on Supercomputing, ICS 2022 Event 36th ACM International Conference on Supercomputing, ICS 2022, 2022-06-27 → 2022-06-30, Virtual, Online Series Proceedings of the International Conference on Supercomputing Part of collection Institutional Repository Document type conference paper Rights © 2022 Taha Shahroodi, M.Z. Zahedi, A. Abhairaj Singh, J.S.S.M. Wong, S. Hamdioui Files PDF 3524059.3532367.pdf 1.43 MB Close viewer /islandora/object/uuid:ae58263f-8732-48dc-91d4-48898852c710/datastream/OBJ/view