Award Abstract # 1664162
SI2-SSI: Pegasus: Automating Compute and Data Intensive Science

NSF Org: OAC
Office of Advanced Cyberinfrastructure (OAC)
Recipient: UNIVERSITY OF SOUTHERN CALIFORNIA
Initial Amendment Date: May 8, 2017
Latest Amendment Date: May 8, 2017
Award Number: 1664162
Award Instrument: Standard Grant
Program Manager: Varun Chandola
OAC
 Office of Advanced Cyberinfrastructure (OAC)
CSE
 Directorate for Computer and Information Science and Engineering
Start Date: May 15, 2017
End Date: September 30, 2023 (Estimated)
Total Intended Award Amount: $2,500,000.00
Total Awarded Amount to Date: $2,500,000.00
Funds Obligated to Date: FY 2017 = $2,500,000.00
History of Investigator:
  • Ewa Deelman (Principal Investigator)
    deelman@isi.edu
  • Miron Livny (Co-Principal Investigator)
Recipient Sponsored Research Office: University of Southern California
3720 S FLOWER ST FL 3
LOS ANGELES
CA  US  90033
(213)740-7762
Sponsor Congressional District: 34
Primary Place of Performance: University of Southern California
4676 Admiralty Way, Suite 1001
Marina del Rey
CA  US  90292-6601
Primary Place of Performance
Congressional District:
36
Unique Entity Identifier (UEI): G88KLJR3KYT5
Parent UEI:
NSF Program(s): Software Institutes
Primary Program Source: 01001718DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 7433, 8009, 8004
Program Element Code(s): 800400
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.070

ABSTRACT

This project addresses the ever-growing gap between the capabilities offered by on-campus and off-campus cyberinfrastructures (CI) and the ability of researchers to effectively harness these capabilities to advance scientific discovery. Faculty and students on campuses struggle to extract knowledge from data that does not fit on their laptops or cannot be processed by an Excel spreadsheet and they find it difficult to efficiently manage their computations. The project sustains and enhances the Pegasus Workflow Management System, which enables scientist to orchestrate and run data- and compute-intensive computations on diverse distributed computational resources. Enhancements focus on the automation capabilities provided by Pegasus to support workflows handling large data sets, as well as usability of Pegasus that lowers the barrier of its adoption. This effort expands the reach of the advanced capabilities provided by Pegasus to researchers from a broader spectrum of disciplines that range from gravitational-wave physics to bioinformatics, and from earth science to material science.

For more than 15 years the Pegasus Workflow Management System has been designed, implemented and supported to provide abstractions that enable scientists to focus on structuring their computations without worrying about the details of the target CI. To support these workflow abstractions Pegasus provides automation capabilities that seamlessly map workflows onto target resources, sparing scientists the overhead of managing the data flow, job scheduling, fault recovery and adaptation of their applications. Automation enables the delivery of services that consider criteria such as time-to-solution, as well as takes into account efficient use of resources, managing the throughput of tasks, and data transfer requests. The power of these abstractions was demonstrated in 2015 when Pegasus was used by an international collaboration to harness a diverse set of resources and to manage compute- and data- intensive workflows that confirmed the existence of gravitational waves, as predicted by Einstein's theory of relativity. Experience from working with diverse scientific domains - astronomy, bioinformatics, climate modeling, earthquake science, gravitational and material science - uncover opportunities for further automation of scientific workflows. This project addresses these opportunities through innovation in the following areas: automation methods to include resource provisioning ahead of and during workflow execution, data-aware job scheduling algorithms, and data sharing mechanisms in high-throughput environments. To support a broader group of "long-tail" scientists, effort is devoted to usability improvements as well as outreach, education, and training activities. The proposed work includes the implementation and evaluation of advanced frameworks, algorithms, and methods that enhance the power of automation in support of data-intensive science. These enhancements are delivers as dependable software tools integrated with Pegasus so that they can be evaluated in the context of real-life applications and computing environments. The data-aware focus targets new classes of applications executing in high-throughput and high-performance environments. Pegasus has been adopted by researchers from a broad spectrum of disciplines that range from gravitational-wave physics to bioinformatics, and from earth science to material science. It provides and enhances access to national CI such as OSG and XSEDE, and as part of this work it will be deployed within Chameleon and Jetstream to provide broader access to NSF's CI investments. Through usability improvements, engagement with CI and community platform providers such as HubZero and Cyverse, combined with educational, training, and tutorial activities, this project broadens the set of researchers that leverage automation for their work. Collaboration with the Gateways Institute assures that Pegasus interfaces are suitable for vertical integration within science gateways and seamlessly supports new scientific communities.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 24)
Do, Tu Mai and Pottier, Loïc and Ferreira da Silva, Rafael and CaínoLores, Silvina and Taufer, Michela and Deelman, Ewa "Performance assessment of ensembles of in situ workflows under resource constraints" Concurrency and Computation: Practice and Experience , 2022 https://doi.org/10.1002/cpe.7111 Citation Details
Krawczuk, Patrycja and Papadimitriou, George and Tanaka, Ryan and Anh Do, Tu Mai and Subramanya, Srujana and Nagarkar, Shubham and Jain, Aditi and Lam, Kelsie and Mandal, Anirban and Pottier, Loic and Deelman, Ewa "A Performance Characterization of Scientific Machine Learning Workflows" 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), , 2021 https://doi.org/10.1109/WORKS54523.2021.00013 Citation Details
Lyons, Eric and Seo, Dong-Jun and Kim, Sunghee and Habibi, Hamideh and Papadimitriou, George and Tanaka, Ryan and Deelman, Ewa and Zink, Michael and Mandal, Anirban "Predicting Flash Floods in the Dallas-Fort Worth Metroplex Using Workflows and Cloud Computing" 2021 IEEE 17th International Conference on eScience (eScience) , 2021 https://doi.org/10.1109/eScience51609.2021.00050 Citation Details
Morel, Alicia Esquivel and Qu, Chengyi and Calyam, Prasad and Wang, Cong and Thareja, Komal and Mandal, Anirban and Lyons, Eric and Zink, Michael and Papadimitriou, George and Deelman, Ewa "FlyNet: Drones on the Horizon" IEEE Internet Computing , v.27 , 2023 https://doi.org/10.1109/MIC.2023.3260440 Citation Details
Osinski, Tomasz and Rynge, Mats and Hong, James K. and Vahi, Karan and Chu, Ruilin and Sul, Cesar and Deelman, Ewa and Kim, Byoung-Do "An automated Cryo-EM computational environment on the HPC system using Pegasus WMS" 2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS) , 2022 https://doi.org/10.1109/WORKS56498.2022.00013 Citation Details
Papadimitriou, G. "Lightweight GPU Monitoring Extension for Pegasus Kickstart" 2021 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS). , 2021 https://doi.org/10.5281/zenodo.5915106 Citation Details
Pottier, Loic and Ferreira da Silva, Rafael and Casanova, Henri and Deelman, Ewa "Modeling the Performance of Scientific Workflow Executions on HPC Platforms with Burst Buffers" 2020 IEEE International Conference on Cluster Computing (CLUSTER) , 2020 https://doi.org/10.1109/CLUSTER49012.2020.00019 Citation Details
Silva, Rafael Ferreira and Mayani, Rajiv and Shi, Yuning and Kemanian, Armen R. and Rynge, Mats and Deelman, Ewa "Empowering Agroecosystem Modeling with HTC Scientific Workflows: The Cycles Model Use Case" First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD) , 2019 10.1109/BigData47090.2019.9006107 Citation Details
Silva, Rafael Ferreira and Pottier, Loic and Coleman, Taina and Deelman, Ewa and Casanova, Henri "WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development" 2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS) , 2020 https://doi.org/10.1109/WORKS51914.2020.00012 Citation Details
Tanaka, Ryan and Papadimitriou, George and Viswanath, Sai Charan and Wang, Cong and Lyons, Eric and Thareja, Komal and Qu, Chengyi and Esquivel, Alicia and Deelman, Ewa and Mandal, Anirban and Calyam, Prasad and Zink, Michael "Automating Edge-to-cloud Workflows for Science: Traversing the Edge-to-cloud Continuum with Pegasus" 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid) , 2022 https://doi.org/10.1109/CCGrid54584.2022.00098 Citation Details
T. H. Jordan, S. Callaghan "CyberShake Models of Seismic Hazards in Southern and Central California," Proceedings of the U.S. National Conference on Earthquake Engineering , 2018 Citation Details
(Showing: 1 - 10 of 24)

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

This project funded the development and user support for the Pegasus workflow management system. Pegasus automates the execution of computational workflows on heterogeneous cyberinfrastructure including campus resources, clouds, as well as high-performance and high-throughput computing systems. Pegasus pioneered the use of planning in scientific workflow systems. It enables users to focus on their science by describing their workflows in a resource-independent way. Pegasus takes that description and automatically maps the tasks onto heterogeneous resources, determines the necessary data transfers between tasks, and optimizes the workflow for performance and reliability. The result is an executable workflow that includes compute job submit scripts and data management jobs for the target cyberinfrastructure. Pegasus has a notion of the submit host from where the system submits jobs to multiple distributed resources within the national cyberinfrastructure ecosystem.  Pegasus workflows are easy to compose using Python APIs and Jupyter Notebook interfaces and are portable across heterogeneous cyberinfrastructure.

As part of this project, Pegasus enabled a wide variety of researchers to make scientific breakthroughs. Researchers from the Southern California Earthquake Center have used Pegasus to generate state-of-the-art physics-based seismic hazard maps of California. These maps can inform how the next generation of civil infrastructure needs to be designed and built. They can help insurance companies assess earthquake risk and can enable disaster planners to adequately prepare for significant earthquakes. Pegasus provided community resources to create better soybeans and enabled policymakers to make decisions about land and water usage. Pegasus powers CASA weather radar workflows, providing time-critical information during severe weather events in the Dallas Fort Worth area.  The Event Horizon Telescope project uses it to simulate Black Holes, and other astronomers use it to generate mosaics of the galactic plane. Pegasus was also adapted to enable real time experimental data analysis. For example, Pegasus does real-time 3D reconstruction of biological samples as scientists run their experiments at USC’s Cryo-EM facility, greatly improving result quality.

This project supported these and other applications by enhancing Pegasus' capabilities, enabling it to support novel cyberinfrastructure, and providing hands-on support to scientists.

 

 


Last Modified: 01/21/2024
Modified by: Ewa Deelman

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