Investigando o Impacto de Containers no Desempenho de um Workflow Científico
Abstract
The description of scientific workflows through a standard language provides, among other things, portability and scalability to scientific workflows. Meeting portability and reproducibility, containers represent a lightweight virtualization. Thus, we propose an investigation of the impacts of containers on the performance of scientific workflows through the execution of Hecil. The Toil workflow engine reads and executes the Hecil workflow and we present two containerized strategies for task scheduling. The results shows that Toil creation and removal of containers can represent a bottleneck in the execution of workflows.References
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Xavier, M. G., Neves, M. V., Rossi, F. D., Ferreto, T. C., Lange, T., and De Rose, C. A. F. (2013). Performance evaluation of container-based virtualization for high perfor- mance computing environments. In 2013 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, pages 233–240.
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1st ACM SIGMOD Workshop on Scalable Workow Execution Engines and Technolo- gies, SWEET '12, New York, NY, USA. Association for Computing Machinery.
Chapman, B., Chilton, J., Heuer, M., Kartashov, A., Leehr, D., Ménager, H., Nedeljko- vich, M., Scales, M., Soiland-Reyes, S., and Stojanovic, L. (2016). Common Workow Language, v1.0. Specication, product of the Common Workow Language working group. http://www.commonwl.org/v1.0/.
Combe, T., Martin, A., and Di Pietro, R. (2016). To Docker or not to Docker: A security perspective. IEEE Cloud Computing, 3(5):54–62.
Dua, R., Raja, A. R., and Kakadia, D. (2014). Virtualization vs containerization to support PaaS. In 2014 IEEE International Conference on Cloud Engineering, pages 610–614.
Felter, W., Ferreira, A., Rajamony, R., and Rubio, J. (2015). An updated performance In 2015 IEEE International comparison of virtual machines and Linux containers. Symposium on Performance Analysis of Systems and Software (ISPASS), pages 171– 172.
Hung, L.-H., Hu, J., Meiss, T., Ingersoll, A., Lloyd, W., Kristiyanto, D., Xiong, Y., Sobie, E., and Yeung, K. Y. (2018). Building containerized workows using the biodepot- workow-builder (bwb). bioRxiv.
Jansen, C., Annuscheit, J., Schilling, B., Strohmenger, K., Witt, M., Bartusch, F., Herta, C., Hufnagl, P., and Krefting, D. (2020). Curious containers: A framework for com- putational reproducibility in life sciences with support for deep learning applications. Future Generation Computer Systems, 112:209 – 227.
Perez-Riverol, Y. and Moreno, P. (2019). Scalable data analysis in proteomics and meta- bolomics using biocontainers and workows engines. bioRxiv.
Preeth E N, Mulerickal, F. J. P., Paul, B., and Sastri, Y. (2015). Evaluation of Docker containers based on hardware utilization. In 2015 International Conference on Control Communication Computing India (ICCC), pages 697–700.
Stefansen, C. (2005). Smawl: A small workow language based on ccs. Technical report, Harvard Computer Science Group Technical Report TR-06-05.
Sweeney, K. M. D. and Thain, D. (2018). Efcient integration of containers into scien- tic workows. In Proceedings of the 9th Workshop on Scientic Cloud Computing, ScienceCloud'18, pages 7:1–7:6, New York, NY, USA. ACM.
van der Aalst, W. and ter Hofstede, A. (2005). Yawl: yet another workow language. Information Systems, 30(4):245 – 275.
Xavier, M. G., Neves, M. V., Rossi, F. D., Ferreto, T. C., Lange, T., and De Rose, C. A. F. (2013). Performance evaluation of container-based virtualization for high perfor- mance computing environments. In 2013 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, pages 233–240.
Zheng, C. and Thain, D. (2015). Integrating containers into workows: A case study using Makeow, Work Queue, and Docker. In Proceedings of the 8th International Workshop on Virtualization Technologies in Distributed Computing, VTDC '15, pages 31–38, New York, NY, USA. ACM.
Published
2020-10-21
How to Cite
ALVES, Bruno; CHARÃO, Andrea.
Investigando o Impacto de Containers no Desempenho de um Workflow Científico. In: UNDERGRADUATE RESEARCH WORKSHOP - SYMPOSIUM ON HIGH PERFORMANCE COMPUTING SYSTEMS (SSCAD), 21. , 2020, Evento Online.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2020
.
p. 117-124.
DOI: https://doi.org/10.5753/wscad_estendido.2020.14097.
