A performance evaluation of X-ray crystallography scientific workflow using scicumulus

Proceedings - 2011 IEEE 4th International Conference on Cloud Computing, CLOUD 2011

Volumn , Issue , 2011, Pages 708-715

  De Oliveira, Daniel ^a   Ocaña, Kary ^a   Ogasawara, Eduardo ^b   Dias, Jonas ^b   Baião, Fernanda ^c   Mattoso, Marta ^c  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b FEDERAL UNIVERSITY OF THE STATE OF RIO DE JANEIRO   (Brazil)

^c CENTRO FEDERAL DE EDUCAÇÃO TECNOLÓGICA CELSO SUCKOW DA FONSECA   (Brazil)

Author keywords

Cloud Computing; Scientific workflows

Indexed keywords

AMAZON EC2; COMPARATIVE GENOMICS; DRUG DISCOVERY; EXECUTION TIME; HIGH-PERFORMANCE COMPUTING; INPUT DATAS; MONETARY COSTS; ORTHOLOGS; PARALLEL EXECUTIONS; PARALLELIZING; PERFORMANCE EVALUATION; PHYLOGENOMICS; SCIENTIFIC WORKFLOWS; THREE-DIMENSIONAL STRUCTURE; WORK-FLOWS;

BIOINFORMATICS; COMPUTER SOFTWARE SELECTION AND EVALUATION; EXPERIMENTS; MANAGEMENT; MIDDLEWARE; MINERALOGY; SELF ASSEMBLY; WORK SIMPLIFICATION; X RAY CRYSTALLOGRAPHY; X RAYS;

CLOUD COMPUTING;

EID: 80053163256     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CLOUD.2011.99     Document Type: Conference Paper

References (25)

1. S.F. Campbell, 2000, Science, art and drug discovery: a personal perspective, Clinical Science (London, England: 1979), v. 99, n. 4 (Oct.), p. 255-260.
2. E.S. Lander, 2001, Initial sequencing and analysis of the human genome, Nature, v. 409, n. 6822 (Feb.), p. 860-921. (Pubitemid 32165345)
3. G.C. Terstappen and A. Reggiani, 2001, In silico research in drug discovery, Trends in Pharmacological Sciences, v. 22, n. 1 (Jan.), p. 23-26. (Pubitemid 32126282)
4. I.J. Taylor, E. Deelman, D.B. Gannon, M. Shields, and (Eds.), 2007, Workflows for e-Science: Scientific Workflows for Grids. 1 ed. Springer.
5. E. Walker and C. Guiang, 2007, Challenges in executing large parameter sweep studies across widely distributed computing environments, In: Workshop on Challenges of large applications in distributed environments, p. 11-18, Monterey, California, USA. (Pubitemid 47315531)
6. TOP500, 2010, TOP500 Supercomputing Sites, http://www.top500.org/.
7. D. Oliveira, F. Baião, and M. Mattoso, 2010, "Towards a Taxonomy for Cloud Computing from an e-Science Perspective", Cloud Computing: Principles, Systems and Applications, Heidelberg: Springer-Verlag
8. T. Hey, S. Tansley, and K. Tolle, 2009, The Fourth Paradigm: Data-Intensive Scientific Discovery. Online book, Url.: http:// emotionalcompetency.com/sci/booktoc.html.
9. D. Oliveira, E. Ogasawara, F. Baião, and M. Mattoso, 2010, SciCumulus: A Lightweigth Cloud Middleware to Explore Many Task Computing Paradigm in Scientific Workflows, In: Proc. 3rd IEEE International Conference on Cloud Computing, Miami, FL.
10. I. Raicu, I. Foster, and Yong Zhao, 2008, Many-task computing for grids and supercomputers, In: Workshop on Many-Task Computing on Grids and Supercomputers, p. 1-11, Austin, Texas.
11. Y. El-Khamra, H. Kim, S. Jha, and M. Parashar, 2010, Exploring the Performance Fluctuations of HPC Workloads on Clouds, In: Proceedings of the 2010 IEEE Second International Conference on Cloud Computing Technology and Science, p. 383-387, Washington, DC, USA.
12. K.R. Jackson, L. Ramakrishnan, K. Muriki, S. Canon, S. Cholia, J. Shalf, H.J. Wasserman, and N.J. Wright, 2010, Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud, In: Proceedings of the 2010 IEEE Second International Conference on Cloud Computing Technology and Science, p. 159-168, Washington, DC, USA.
13. Q. He, S. Zhou, B. Kobler, D. Duffy, and T. McGlynn, 2010, Case study for running HPC applications in public clouds, In: Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, p. 395-401, New York, NY, USA.
14. Amazon EC2, 2010. Amazon Elastic Compute Cloud (Amazon EC2). Amazon Elastic Compute Cloud (Amazon EC2). URL: http://aws.amazon.com/ec2/. Access: 5 Mar 2010.
15. L.A. Meyer, S.C. Rössle, P.M. Bisch, and M. Mattoso, 2005, "Parallelism in Bioinformatics Workflows", High Performance Computing for Computational Science - VECPAR 2004, p. 583-597. (Pubitemid 41241334)
16. S.P. Callahan, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, and H.T. Vo, 2006, VisTrails: visualization meets data management, In: Proc. SIGMOD 2006, p. 745-747, Chicago, Illinois, USA. (Pubitemid 46946568)
17. Mark Baker, Bryan Carpenter, and Aamir Shafi. MPJ: Enabling Parallel Simulations in Java, URL: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1. 1.95.4699 Access: 31 Jan 2011
18. K.R. Jackson, L. Ramakrishnan, K.J. Runge, and R.C. Thomas, 2010, Seeking supernovae in the clouds: a performance study, In: Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, p. 421-429, New York, NY, USA.
19. SubCloud, 2011. Shared Enterprise File System for Amazon S3 Cloud Storage | SubCloud. URL: http://www.subcloud.com/. Access: 31 Jan 2011.
20. W.M.P.V.D. Aalst, A.H.M.T. Hofstede, B. Kiepuszewski, and A.P. Barros, 2003, Workflow Patterns, Distrib. Parallel Databases, v. 14, n. 1, p. 5-51.
21. E. Deelman, G. Singh, M. Livny, B. Berriman, and J. Good, 2008, The cost of doing science on the cloud: the Montage example, In: SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing, p. 1-12, Austin, Texas.
22. E. Deelman, G. Mehta, G. Singh, M. Su, and K. Vahi, 2007, "Pegasus: Mapping Large-Scale Workflows to Distributed Resources", Workflows for e-Science, Springer, p. 376-394.
23. D. Warneke and O. Kao, 2009, Nephele: efficient parallel data processing in the cloud, In: Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers, p. 8:1-8:10, New York, NY, USA.
24. A. Matsunaga, M. Tsugawa, and J. Fortes, 2008, CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications, IEEE eScience 2008, p. 229, 222.
25. F. Coutinho, E. Ogasawara, D. Oliveira, V. Braganholo, A.A.B. Lima, A.M.R. Dávila, and M. Mattoso, 2010, Data Parallelism in Bioinformatics Workflows Using Hydra, In: ECMLS 2010, Chicago, Illinois, United States.