A performance evaluation of sequence alignment software in virtualized environments

Zachary J. Estrada, Zachary Stephens, Cuong Pham, Zbigniew T Kalbarczyk, Ravishankar K Iyer

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

Abstract

The prospect of simpler infrastructure management and affordability has garnered interest in cloud computing from bioinformaticians. However, the performance cost of adopting such an infrastructure model for bioinformatics is not fully known. In an effort to help quantify this performance cost, we ran synthetic benchmarks and measured the runtimes of two short-read alignment applications on cloud-like virtualization environments. The environments were implemented utilizing the KVM hypervisor, the Xen hypervisor, and Linux Containers. We compare the runtime in each environment against a physical server and offer discussion and insights. Though the applications perform similar operations, we observe that their performance characteristics differ, as do their performance in the different virtualized environments. We attribute the differences to the way that these programs utilize system resources. We find that the more CPU-bound Novo align is much less sensitive to virtualization environments than BWA is, and has near-physical server performance even when virtualized. Additionally, we find that static CPU pinning can improve performance, and we demonstrate that Linux Containers offer performance comparable to that of a physical server.

Original languageEnglish (US)
Title of host publicationProceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014
PublisherIEEE Computer Society
Pages730-737
Number of pages8
ISBN (Print)9781479927838
DOIs
StatePublished - Jan 1 2014
Event14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGrid 2014 - Chicago, IL, United States
Duration: May 26 2014May 29 2014

Publication series

NameProceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014

Other

Other14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGrid 2014
CountryUnited States
CityChicago, IL
Period5/26/145/29/14

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Keywords

  • KVM
  • Linux containers
  • Xen
  • bioinformatics
  • cloud computing
  • container based virtualization
  • genomics
  • high performance computing
  • sequence alignment
  • virtualization

ASJC Scopus subject areas

  • Software

Cite this

Estrada, Z. J., Stephens, Z., Pham, C., Kalbarczyk, Z. T., & Iyer, R. K. (2014). A performance evaluation of sequence alignment software in virtualized environments. In Proceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014 (pp. 730-737). [6846525] (Proceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014). IEEE Computer Society. https://doi.org/10.1109/CCGrid.2014.125