A dynamic energy-aware model for scheduling computationally intensive bioinformatics applications

Sachin Pawaskar, Hesham H Ali

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

3 Scopus citations

Abstract

High Performance Computing (HPC) resources are housed in large datacenters, which consume huge amounts of energy and are quickly demanding attention from businesses as they result in high operating costs. On the other hand HPC environments have been very useful to researchers in many emerging areas in life sciences such as Bioinformatics and Medical Informatics. In this paper, we provide a dynamic model for energy aware scheduling (EAS) in a HPC environment; we use a widely used bioinformatics tool named BLAT (BLAST-like alignment tool) running in a HPC environment as our case study. Our proposed EAS model incorporates 2-Phases: an Offline phase and an Online one. In the Offline Phase, we use sequences gathered from researchers and parallelize the runs to understand the run (speedup) profile of the program. The EAS Engine then utilizes such information to generate the initial schedule. In the Online Phase a feedback mechanism is incorporated between the EAS Engine and the master scheduling process. As scheduled tasks are completed, their actual execution time (AET) is used to adjust the resources required for scheduling remaining tasks using the least number of nodes while meeting a given deadline. The conducted experiments show that the proposed approach succeeded in meeting preset deadlines while minimizing the number of nodes; thus reducing overall energy utilized.

Original languageEnglish (US)
Title of host publicationProceedings of the 2010 International Conference on High Performance Computing and Simulation, HPCS 2010
Pages216-223
Number of pages8
DOIs
StatePublished - Sep 28 2010
Event2010 International Conference on High Performance Computing and Simulation, HPCS 2010 - Caen, France
Duration: Jun 28 2010Jul 2 2010

Publication series

NameProceedings of the 2010 International Conference on High Performance Computing and Simulation, HPCS 2010

Conference

Conference2010 International Conference on High Performance Computing and Simulation, HPCS 2010
CountryFrance
CityCaen
Period6/28/107/2/10

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Keywords

  • Algorithms
  • Bioinformatics
  • Energy awareness
  • High Performance Computing
  • Parallel processing
  • Scheduling

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Software

Cite this

Pawaskar, S., & Ali, H. H. (2010). A dynamic energy-aware model for scheduling computationally intensive bioinformatics applications. In Proceedings of the 2010 International Conference on High Performance Computing and Simulation, HPCS 2010 (pp. 216-223). [5547133] (Proceedings of the 2010 International Conference on High Performance Computing and Simulation, HPCS 2010). https://doi.org/10.1109/HPCS.2010.5547133