research-article

dispel4py: a Python framework for data-intensive scientific computing

Authors:

Rosa Filguiera,

Iraklis Klampanos,

Alexander Moreno,

Malcolm AtkinsonAuthors Info & Claims

DISCS '14: Proceedings of the 2014 International Workshop on Data Intensive Scalable Computing Systems

Pages 9 - 16

https://doi.org/10.1109/DISCS.2014.12

Published: 16 November 2014 Publication History

Abstract

This paper presents dispel4py, a new Python framework for describing abstract stream-based workflows for distributed data-intensive applications. The main aim of dispel4py is to enable scientists to focus on their computation instead of being distracted by details of the computing infrastructure they use. Therefore, special care has been taken to provide dispel4py with the ability to map abstract workflows to different enactment platforms dynamically, at run time. In this work we present four dispel4py mappings: Apache Storm, MPI, multi-threading and sequential. The results show that dispel4py is successful in enacting on different platforms, while also providing scalable performance.

References

[1]

A. J. G. Hey, S. Tansley, and K. Tolle, The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, 2009.

[2]

T. Segaran and J. Hammerbacher, Beautiful Data: The Stories Behind Elegant Data Solutions. O'Reilly, 2009.

[3]

A. Shoshani and D. Rotem, Scientific Data Management: Challenges, Technology and Deployment, ser. Computational Science Series. Chapman and Hall/CRC, 2010.

Digital Library

[4]

W. H. Dutton and P. W. Jeffreys, World Wide Research: Reshaping the Sciences and Humanities. MIT Press, 2010.

Digital Library

[5]

T. Oinn, M. Addis, J. Ferris, D. Marvin, M. Senger, M. Greenwood, T. Carver, K. Glover, M. R. Pocock, A. Wipat, and P. Li, "Taverna: A tool for the composition and enactment of bioinformatics workflows," Bioinformatics, vol. 20, no. 17, pp. 3045--3054, Nov. 2004. {Online}. Available: http://dx.doi.org/10.1093/bioinformatics/bth361

Digital Library

[6]

D. De Roure and C. Goble, "Software design for empowering scientists," IEEE Software, vol. 26, no. 1, pp. 88--95, 2009.

Digital Library

[7]

M. P. Atkinson, C. S. Liew, M. Galea, P. Martin, A. Krause, A. Mouat,. Corcho, and D. Snelling, "Data-intensive architecture for scientific knowledge discovery." Distributed and Parallel Databases, vol. 30, no. 5-6, pp. 307--324, 2012. {Online}. Available: http://dblp.uni-trier.de/db/journals/dpd/dpd30.html#AtkinsonLGMKMCS12

Digital Library

[8]

Message Passing Interface Forum, "MPI: A message-passing interface standard," International Journal of Supercomputer Applications, vol. 8, pp. 165--414, 1994.

[9]

I. Altintas, C. Berkley, E. Jaeger, M. Jones, B. Ludascher, and S. Mock, "Kepler: an extensible system for design and execution of scientific workflows," in Proceedings of 16th International Conference on Scientific and Statistical Database Management, June 2004, pp. 423--424.

Digital Library

[10]

E. Deelman, G. Singh, M.-H. Su, J. Blythe, Y. Gil, C. Kesselman, G. Mehta, K. Vahi, G. B. Berriman, J. Good, A. C. Laity, J. C. Jacob, and D. S. Katz, "Pegasus: A framework for mapping complex scientific workflows onto distributed systems," Scientific Programming, vol. 13, no. 3, pp. 219--237, 2005.

Digital Library

[11]

D. Churches, G. Gombas, A. Harrison, J. Maassen, C. Robinson, M. Shields, I. Taylor, and I. Wang, "Programming scientific and distributed workflow with Triana services: Research Articles," Concurrency and Computation: Practice and Experience, vol. 18, no. 10, pp. 1021--1037, 2006.

Digital Library

[12]

M. Wilde, M. Hategan, J. M. Wozniak, B. Clifford, D. S. Katz, and I. Foster, "Swift: A language for distributed parallel scripting," Parallel Computing, vol. 37, no. 9, pp. 633--652, 2011. {Online}. Available: http://www.sciencedirect.com/science/article/pii/S0167819111000524

Digital Library

[13]

Y. Simmhan, R. Barga, C. van Ingen, E. Lazowska, and A. Szalay, "Building the Trident Scientific Workflow Workbench for Data Management in the Cloud," in International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP). IEEE, October 2009.

Digital Library

[14]

X. Llorá, B. Ács, L. S. Auvil, B. Capitanu, M. E. Welge, and D. E. Goldberg, "Meandre: Semantic-Driven Data-Intensive Flows in the Clouds," in IEEE Fourth International Conference on eScience. IEEE Press, 2008, pp. 238--245.

Digital Library

[15]

Z. Falt, D. Bednárek, M. Kruliš, J. Yaghob, and F. Zavoral, "Bobolang: A language for parallel streaming applications," in Proceedings of the 23rd International Symposium on High-performance Parallel and Distributed Computing, ser. HPDC '14. New York, NY, USA: ACM, 2014, pp. 311--314. {Online}. Available: http://doi.acm.org/10.1145/2600212.2600711

Digital Library

[16]

P. Fraternali and S. Paraboschi, "Chimera: A language for designing rule applications." in Active Rules in Database Systems, 1999, pp. 309--322. {Online}. Available: http://dblp.uni-trier.de/db/books/collections/patton99.html#FraternaliP99

[17]

G. D. Bensen, M. H. Ritzwoller, M. P. Barmin, A. L. Levshin, F. Lin, M. P. Moschetti, N. M. Shapiro, and Y. Yang, "Processing seismic ambient noise data to obtain reliable broad-band surface wave dispersion measurements," Geophysical Journal International, vol. 169, no. 3, pp. 1239--1260, 2007.

[18]

"SEED Reference Manual v2.4, Appendix G: Data Only SEED Volumes (Mini-SEED)," http://www.iris.edu/manuals/SEED_appG.htm, accessed August 2011.

Cited By

Zhao RAtkinson MPapapanagiotou PMagnoni FFleuriot J(2021)Dr.Aid: Supporting Data-governance Rule Compliance for Decentralized Collaboration in an Automated WayProceedings of the ACM on Human-Computer Interaction10.1145/34796045:CSCW2(1-43)Online publication date: 18-Oct-2021
https://dl.acm.org/doi/10.1145/3479604
Pimentel JFreire JMurta LBraganholo V(2019)A Survey on Collecting, Managing, and Analyzing Provenance from ScriptsACM Computing Surveys10.1145/331195552:3(1-38)Online publication date: 18-Jun-2019
https://dl.acm.org/doi/10.1145/3311955
Filgueira Rda Silva RKrause ADeelman EAtkinson M(2016)AsterismProceedings of the 7th International Workshop on Data-Intensive Computing in the Cloud10.5555/3018100.3018101(1-8)Online publication date: 13-Nov-2016
https://dl.acm.org/doi/10.5555/3018100.3018101
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Information & Contributors

Information

Published In

cover image ACM Conferences

DISCS '14: Proceedings of the 2014 International Workshop on Data Intensive Scalable Computing Systems

November 2014

86 pages

ISBN:9781479970384

Conference Chair:
Dries Kimpe
Argonne National Laboratory
,
General Chair:
Yong Chen
Texas Tech University
,
Program Chairs:
Philip C. Roth
Oak Ridge National Laboratory
,
Weikuan Yu
Auburn University

Sponsors

SIGHPC: ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing
IEEE: IEEE Computer Society Technical Committee on Design Automation
ACM: Association for Computing Machinery
SIGARCH: ACM Special Interest Group on Computer Architecture

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IEEE Press

Publication History

Published: 16 November 2014

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Research-article

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SC '14

Sponsor:

SC '14: International Conference for High Performance Computing, Networking, Storage and Analysis

November 16 - 21, 2014

Louisiana, New Orleans

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Overall Acceptance Rate 19 of 34 submissions, 56%

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Cited By

Zhao RAtkinson MPapapanagiotou PMagnoni FFleuriot J(2021)Dr.Aid: Supporting Data-governance Rule Compliance for Decentralized Collaboration in an Automated WayProceedings of the ACM on Human-Computer Interaction10.1145/34796045:CSCW2(1-43)Online publication date: 18-Oct-2021
https://dl.acm.org/doi/10.1145/3479604
Pimentel JFreire JMurta LBraganholo V(2019)A Survey on Collecting, Managing, and Analyzing Provenance from ScriptsACM Computing Surveys10.1145/331195552:3(1-38)Online publication date: 18-Jun-2019
https://dl.acm.org/doi/10.1145/3311955
Filgueira Rda Silva RKrause ADeelman EAtkinson M(2016)AsterismProceedings of the 7th International Workshop on Data-Intensive Computing in the Cloud10.5555/3018100.3018101(1-8)Online publication date: 13-Nov-2016
https://dl.acm.org/doi/10.5555/3018100.3018101
Sánchez-Expósito SMartín PRuiz JVerdes-Montenegro LGarrido JSirvent RFalcó ABadia RLezzi D(2016)Web Services as Building Blocks for Science Gateways in AstrophysicsJournal of Grid Computing10.1007/s10723-016-9382-y14:4(673-685)Online publication date: 1-Dec-2016
https://dl.acm.org/doi/10.1007/s10723-016-9382-y
Krause AFilgueira RAtkinson M(2015)dispel4pyProceedings of the 5th Workshop on Python for High-Performance and Scientific Computing10.1145/2835857.2835863(1-10)Online publication date: 15-Nov-2015
https://dl.acm.org/doi/10.1145/2835857.2835863
Gesing SAtkinson MFilgueira RTaylor IJones AStankovski VLiew CSpinuso ATerstyanszky GKacsuk PMontagnat JTaylor I(2014)Workflows in a dashboardProceedings of the 9th Workshop on Workflows in Support of Large-Scale Science10.1109/WORKS.2014.6(82-93)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/WORKS.2014.6

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