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Disaggregating Non-Volatile Memory for Throughput-Oriented Genomics Workloads

  • Aaron CallEmail author
  • Jordà Polo
  • David Carrera
  • Francesc Guim
  • Sujoy Sen
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11339)

Abstract

Massive exploitation of next-generation sequencing technologies requires dealing with both: huge amounts of data and complex bioinformatics pipelines. Computing architectures have evolved to deal with these problems, enabling approaches that were unfeasible years ago: accelerators and Non-Volatile Memories (NVM) are becoming widely used to enhance the most demanding workloads. However, bioinformatics workloads are usually part of bigger pipelines with different and dynamic needs in terms of resources. The introduction of Software Defined Infrastructures (SDI) for data centers provides roots to dramatically increase the efficiency in the management of infrastructures. SDI enables new ways to structure hardware resources through disaggregation, and provides new hardware composability and sharing mechanisms to deploy workloads in more flexible ways. In this paper we study a state-of-the-art genomics application, SMUFIN, aiming to address the challenges of future HPC facilities.

Keywords

Genomics Disaggregation Composability NVM NVMeOF Characterization Orchestration 

Notes

Acknowledgment

This work is partially supported by the European Research Council (ERC) under the EU Horizon 2020 programme (GA 639595), the Spanish Ministry of Economy, Industry and Competitivity (TIN2015-65316-P) and the Generalitat de Catalunya (2014-SGR-1051).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Aaron Call
    • 1
    • 2
    Email author
  • Jordà Polo
    • 1
  • David Carrera
    • 1
    • 2
  • Francesc Guim
    • 3
  • Sujoy Sen
    • 3
  1. 1.Barcelona Supercomputing Center (BSC)BarcelonaSpain
  2. 2.Universitat Politècnica de Catalunya (UPC)BarcelonaSpain
  3. 3.Intel CorporationSanta ClaraUSA

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