Publication Details

k-Dispatch: A Workflow Management System for the Automated Execution of Biomedical Ultrasound Simulations on Remote Computing Resources

JAROŠ, M.; TREEBY, B.; GEORGIOU, P.; JAROŠ, J. k-Dispatch: A Workflow Management System for the Automated Execution of Biomedical Ultrasound Simulations on Remote Computing Resources. In Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020. New York: Association for Computing Machinery, 2020. p. 1-10. ISBN: 978-1-4503-7993-9.
Czech title
k-Dispatch: Systém správy vědeckých aplikací pro automatické spouštění biomedicínských ultrazvukových simulací na vzdálených výpočetních prostředcích
Type
conference paper
Language
English
Authors
Jaroš Marta, Ing., Ph.D. (DCSY)
Treeby Bradley
Georgiou Panayiotis (FIT)
Jaroš Jiří, doc. Ing., Ph.D. (DCSY)
URL
Keywords

Workflow management system, middleware, HPC as a service, biomedical workflows, automation, container, personalised medicine

Abstract

Therapeutic ultrasound is increasingly being used for applications in oncology, drug delivery, and neurostimulation. In order to adapt the treatment procedures to patient needs, complex physical models have to be evaluated prior to the treatment. These models, however, require intensive computations that can only be satisfied by cloud and HPC facilities. Unfortunately, employing these facilities and executing the required computations is not straightforward even for experienced developers. k-Dispatch is a novel workflow management system aimed at modelling biomedical ultrasound procedures using the open-source k-Wave acoustic toolbox. It allows ultrasound procedures to be uploaded with a single click and provides a notification when the result is ready for download. Inside k-Dispatch, there is a complex workflow management system which decodes the workflow graph, optimizes the workflow execution parameters, submits jobs to remote computing facilities, monitors their progress, and logs the consumed core hours. In this paper, the architecture and deployment of k-Dispatch are discussed, including the approach used for workflow optimization. A key innovation is the use of previous performance data to automatically select the utilised hardware and execution parameters. A review of related work is also given, including workflow management systems, batch schedulers, and cluster simulators.

Published
2020
Pages
1–10
Proceedings
Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020
ISBN
978-1-4503-7993-9
Publisher
Association for Computing Machinery
Place
New York
DOI
10.1145/3394277.3401854
EID Scopus
2-s2.0-85090150136
BibTeX 
@inproceedings{BUT162293,
  author="Marta {Jaroš} and Bradley {Treeby} and Panayiotis {Georgiou} and Jiří {Jaroš}",
  title="k-Dispatch: A Workflow Management System for the Automated Execution of Biomedical Ultrasound Simulations on Remote Computing Resources",
  booktitle="Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020",
  year="2020",
  pages="1--10",
  publisher="Association for Computing Machinery",
  address="New York",
  doi="10.1145/3394277.3401854",
  isbn="978-1-4503-7993-9",
  url="https://dl.acm.org/doi/pdf/10.1145/3394277.3401854"
}
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