Bit-Wise and Multi-GPU Implementations of the DNA Recombination Algorithm

Elnaz Tavakoli Yazdi, Ankur Limaye, Ali Akoglu, Tosiron Adegbija, Adam Buntzman

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

Abstract

The V(D)J recombination is the primary mechanism for generating a diverse repertoire of T-cell receptors (TCRs) essential to the adaptive immune system for recognizing a wide variety of diseases. However, modeling the TCR repertoire is computationally challenging as the total number of TCRs to be generated and processed can exceed 10^18 sequences. We propose a bit-wise implementation of the V(D) J recombination algorithm, which reduces the memory footprint and execution time by factors of 4 and 2, respectively, compared to the state-of-the-art GPU implementation. We also present a multi-GPU implementation, experimentally identify suitable workload partitioning strategies for both single-and multi-GPU implementations, and, finally, expose the relationship between the workload size and limited scalability offered by the algorithm on a cluster with up to eight GPUs. We show that the bit-wise implementation reduces the execution time from 40.5 hours to 19 hours on a single GPU and 4.4 hours on an eight-GPU configuration.

Original languageEnglish (US)
Title of host publicationProceedings - 26th IEEE International Conference on High Performance Computing, HiPC 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages131-140
Number of pages10
ISBN (Electronic)9781728145358
DOIs
StatePublished - Dec 2019
Event26th Annual IEEE International Conference on High Performance Computing, HiPC 2019 - Hyderabad, India
Duration: Dec 17 2019Dec 20 2019

Publication series

NameProceedings - 26th IEEE International Conference on High Performance Computing, HiPC 2019

Conference

Conference26th Annual IEEE International Conference on High Performance Computing, HiPC 2019
Country/TerritoryIndia
CityHyderabad
Period12/17/1912/20/19

Keywords

  • DNA recombination process
  • Graphics Processing Unit (GPU)
  • bit-wise implementation
  • multi-GPU

ASJC Scopus subject areas

  • Hardware and Architecture
  • Information Systems
  • Information Systems and Management
  • Safety, Risk, Reliability and Quality

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