KrakenOnMem: A Memristor-Augmented HW/SW Framework for Taxonomic Profiling

Taha Shahroodi, Mahdi Zahedi, Abhairaj Singh, Stephan Wong, Said Hamdioui

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

8 Citations (Scopus)
52 Downloads (Pure)


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.

Original languageEnglish
Title of host publicationProceedings of the 36th ACM International Conference on Supercomputing, ICS 2022
PublisherAssociation for Computing Machinery (ACM)
Number of pages14
ISBN (Electronic)9781450392815
Publication statusPublished - 2022
Event36th ACM International Conference on Supercomputing, ICS 2022 - Virtual, Online
Duration: 27 Jun 202230 Jun 2022

Publication series

NameProceedings of the International Conference on Supercomputing


Conference36th ACM International Conference on Supercomputing, ICS 2022
CityVirtual, Online


  • (Hash) table lookup
  • Emerging memories
  • In memory Processing
  • Kraken2
  • Taxonomic profiling


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