Abstract
Abstract
Research process automation–the reliable, efficient, and reproducible execution of linked sets of actions on scientific instruments, computers, data stores, and other resources–has emerged as an essential element of modern science. We report here on new services within the Globus research data management platform that enable the specification of diverse research processes as reusable sets of actions, flows, and the execution of such flows in heterogeneous research environments. To support flows with broad spatial extent (e.g., from scientific instrument to remote data center) and temporal extent (from seconds to weeks), these Globus automation services feature: (1) cloud hosting for reliable execution of even long-lived flows despite sporadic failures; (2) a simple specification and extensible asynchronous action provider API, for defining and executing a wide variety of actions and flows involving heterogeneous resources; (3) an event-driven execution model for automating execution of flows in response to arbitrary events; and (4) a rich security model enabling authorization delegation mechanisms for secure execution of long-running actions across distributed resources. These services permit researchers to outsource and automate the management of a broad range of research tasks to a reliable, scalable, and secure cloud platform. We present use cases for Globus automation services, describe their design and implementation, present microbenchmark studies, and review experiences applying the services in a range of applications.
Highlights
• | The research process automation problem, fundamental to modern science, is defined. | ||||
• | A research process automation approach based on cloud-hosted services is proposed. | ||||
• | New Globus automation services are described that implement this approach | ||||
• | Benchmark results and experiences at large scientific instruments are reported. |
- [1] , Autonomous experimentation systems for materials development: A community perspective, Matter 4 (9) (2021) 2702–2726, 10.1016/j.matt.2021.06.036.Google Scholar
- [2] , An object-oriented framework to enable workflow evolution across materials acceleration platforms, Matter 5 (10) (2022) 3124–3134.Google Scholar
- [3] ,
Bridging data center AI systems with edge computing for actionable information retrieval , in: 3rd Workshop on Extreme-Scale Experiment-in-the-Loop Computing, IEEE, 2021, pp. 15–23, 10.1109/XLOOP54565.2021.00008.Google Scholar - [4] , Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action, Int. J. High Perform. Comput. Appl. (2022), 10.1177/10943420221113.Google Scholar
- [5] , Web Services Business Process Execution Language Version 2.0 primer, 2007, OASIS Specification.Google Scholar
- [6] Conductor scalable workflow orchestration, 2022, https://conductor.netflix.com. (Accessed November 2022).Google Scholar
- [7] D. Xin, et al., How Developers Iterate on Machine Learning Workflows, in: IDEA Workshop at KDD, 2018.Google Scholar
- [8] , Efficient and secure transfer, synchronization, and sharing of big data, IEEE Cloud Comput. 1 (3) (2014) 46–55, 10.1109/MCC.2014.52.Google Scholar
- [9] Amazon States Language, 2022, https://states-language.net/. (Accessed January 2022).Google Scholar
- [10] ,
Globus auth: A research identity and access management platform , in: 12th IEEE International Conference on e-Science, 2016, pp. 203–212, 10.1109/eScience.2016.7870901.Google Scholar - [11] , Globus platform-as-a-service for collaborative science applications, Concurr. Comput.: Pract. Exper. 27 (2) (2015) 290–305, 10.1002/cpe.3262.Google Scholar
- [12] , Linking scientific instruments and computation: Patterns, technologies, and experiences, Patterns 3 (10) (2022), 10.1016/j.patter.2022.100606.Google Scholar
- [13] ,
High-performance ptychographic reconstruction with federated facilities , in: Smoky Mountains Computational Sciences and Engineering Conference, Springer, 2021, pp. 173–189. https://arxiv.org/abs/2111.11330.Google Scholar - [14] , A data ecosystem to support machine learning in materials science, MRS Commun. 9 (4) (2019) 1125–1133, 10.1557/mrc.2019.118.Google Scholar
- [15] , Making Common Fund data more findable: Catalyzing a data ecosystem, 2021,10.1101/2021.11.05.467504. BioRxiv, Cold Spring Harbor Laboratory.Google Scholar
- [16] , Fixed-target serial crystallography at the Structural Biology Center, J. Synchrotron Radiat. 29 (5) (2022) 1141–1151, 10.1107/S1600577522007895.Google Scholar
- [17] ,
Ultrafast focus detection for automated microscopy , in: International Conference on Computational Science, Springer, 2022, pp. 403–416, 10.1109/eScience51609.2021.00039.Google Scholar - [18] , FairDMS: Rapid model training by data and model reuse, 2022, https://arxiv.org/abs/2204.09805.Google Scholar
- [19] ,
Serial synchrotron X-ray crystallography (SSX) , in: Protein Crystallography, Springer, 2017, pp. 239–272.Google Scholar - [20] , DIALS: Implementation and evaluation of a new integration package, Acta Crystallogr. Section D 74 (2) (2018) 85–97, 10.1107/S2059798317017235.Google Scholar
- [21] , Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals, Elife 4 (2015).Google Scholar
- [22] , MemXCT: Design, optimization, scaling, and reproducibility of X-ray tomography imaging, IEEE Trans. Parallel Distrib. Syst. 33 (9) (2021) 2014–2031, 10.1109/TPDS.2021.3128032.Google Scholar
- [23] , TomoGAN: Low-dose synchrotron X-ray tomography with generative adversarial networks, J. Opt. Soc. Amer. A 37 (3) (2020) 422–434, 10.1364/JOSAA.375595.Google Scholar
- [24] , From femtoseconds to hours–measuring dynamics over 18 orders of magnitude with coherent X-rays, Appl. Sci. 11 (13) (2021) 6179.Google Scholar
- [25] , Superresolution imaging via ptychography, J. Opt. Soc. Amer. A 28 (4) (2011) 604–612.Google Scholar
- [26] ,
Overview of high-energy X-ray diffraction microscopy (HEDM) for mesoscale material characterization in three-dimensions , in: Materials Discovery and Design, Springer International Publishing, 2018, pp. 167–201, 10.1007/978-3-319-99465-9_7.Google Scholar - [27] , Cryo-EM—The first thirty years, J. Microsc. 245 (3) (2012) 221–224.Google Scholar
- [28] , Enabling real-time multi-messenger astrophysics discoveries with deep learning, Nat. Rev. Phys. 1 (10) (2019) 600–608, 10.1038/s42254-019-0097-4.Google Scholar
- [29] , Far-field high-energy diffraction microscopy: A tool for intergranular orientation and strain analysis, J. Strain Anal. Eng. Des. 46 (7) (2011) 527–547.Google Scholar
- [30] MIDAS, microstructural imaging using diffraction analysis software, 2022, https://www.aps.anl.gov/Science/Scientific-Software/MIDAS. (Accessed March 2022).Google Scholar
- [31] , The Materials Data Facility: Data services to advance materials science research, JOM 68 (8) (2016) 2045–2052, 10.1007/s11837-016-2001-3.Google Scholar
- [32] ,
DLHub: Model and data serving for science , in: 33rd IEEE International Parallel and Distributed Processing Symposium, 2019, pp. 283–292, 10.1109/IPDPS.2019.00038.Google Scholar - [33] , DLHub: Simplifying publication, discovery, and use of machine learning models in science, J. Parallel Distrib. Comput. 147 (2021) 64–76.Google Scholar
- [34] Common Fund Data Ecosystem (CFDE), https://commonfund.nih.gov/dataecosystem.Google Scholar
- [35] ,
Petrel: A programmatically accessible research data service , in: Practice and Experience in Advanced Research Computing, ACM, 2019, pp. 1–7, 10.1145/3332186.3332241.Google ScholarDigital Library - [36] , Improved protein structure prediction using potentials from deep learning, Nature 577 (7792) (2020) 706–710, 10.1038/s41586-019-1923-7.Google Scholar
- [37] , Globus Nexus: A platform-as-a-service provider of research identity, profile, and group management, Future Gener. Comput. Syst. 56 (2016) 571–583, 10.1016/j.future.2015.09.006.Google ScholarDigital Library
- [38] , Software as a service for data scientists, Commun. ACM 55 (2) (2012) 81–88, 10.1145/2076450.2076468.Google ScholarDigital Library
- [39] ,
Globus platform services for data publication , in: Practice and Experience on Advanced Research Computing, ACM, 2018, pp. 14:1–14:7, 10.1145/3219104.3219127.Google ScholarDigital Library - [40] ,
An open ecosystem for pervasive use of persistent identifiers , in: Practice and Experience in Advanced Research Computing, ACM, 2020, pp. 99–105, 10.1145/3311790.3396660.Google ScholarDigital Library - [41] ,
FuncX: A federated function serving fabric for science , in: 29th International Symposium on High-Performance Parallel and Distributed Computing, 2020, pp. 65–76, 10.1145/3369583.3392683.Google ScholarDigital Library - [42] , FuncX: Federated function as a service for science, IEEE Trans. Parallel Distrib. Syst. 33 (12) (2022) 4948–4963, 10.1109/TPDS.2022.3208767.Google Scholar
- [43] ,
OAuth SSH with globus auth , in: Practice and Experience in Advanced Research Computing, ACM, 2020, pp. 34–40, 10.1145/3311790.3396658.Google ScholarDigital Library - [44] Globus Action Providers, 2022, https://docs.globus.org/api/flows/hosted-action-providers/. (Accessed August 2022).Google Scholar
- [45] AWS Step Functions Visual workflows for modern applications, 2022, https://aws.amazon.com/step-functions. (Accessed January 2022).Google Scholar
- [46] , JSON Schema: A Media Type for Describing JSON Documents, Internet Engineering Task Force, 2020, Work in Progress.Google Scholar
- [47] , OAuth 2.0 Authorization Framework Specification, no. 6749, Internet Engineering Task Force, 2012, http://tools.ietf.org/html/rfc6749.Google Scholar
- [48] Globus action provider tools, 2022, https://action-provider-tools.readthedocs.io/. (Accessed August 2022).Google Scholar
- [49] Existing workflow systems, 2022, https://s.apache.org/existing-workflow-systems. (Accessed January 2022).Google Scholar
- [50] , Scientific workflow management and the Kepler system, Concurr. Comput.: Pract. Exper. 18 (10) (2006) 1039–1065.Google Scholar
- [51] , Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol. 11 (8) (2010) 1–13.Google Scholar
- [52] , Pegasus, a workflow management system for science automation, Future Gener. Comput. Syst. 46 (2015) 17–35.Google ScholarDigital Library
- [53] M. Albrecht, et al., Makeflow: A portable abstraction for data intensive computing on clusters, clouds, and grids, in: 1st ACM SIGMOD Workshop on Scalable Workflow Execution Engines and Technologies, 2012, pp. 1–13.Google Scholar
- [54] ,
Parsl: Pervasive parallel programming in Python , in: 28th International Symposium on High-Performance Parallel and Distributed Computing, ACM, 2019, pp. 25–36, 10.1145/3307681.3325400.Google ScholarDigital Library - [55] ,
A community roadmap for scientific workflows research and development , in: IEEE Workshop on Workflows in Support of Large-Scale Science, 2021, pp. 81–90, 10.1109/WORKS54523.2021.00016.Google Scholar - [56] , Scientific workflows: Moving across paradigms, ACM Comput. Surv. 49 (4) (2016) 1–39.Google ScholarDigital Library
- [57] , A taxonomy and survey of grid resource management systems for distributed computing, Softw. - Pract. Exp. 32 (2) (2002) 135–164.Google Scholar
- [58] , Workflows and e-Science: An overview of workflow system features and capabilities, Future Gener. Comput. Syst. 25 (5) (2009) 528–540.Google ScholarDigital Library
- [59] , Swift: A language for distributed parallel scripting, Parallel Comput. 37 (9) (2011) 633–652, 10.1016/j.parco.2011.05.005.Google ScholarDigital Library
- [60] , Taverna: A tool for building and running workflows of services, Nucleic Acids Res. 34 (suppl_2) (2006) W729–W732.Google Scholar
- [61] , Unraveling the Web services web: An introduction to SOAP, WSDL, and UDDI, IEEE Internet Comput. 6 (2) (2002) 86–93.Google Scholar
- [62] ,
A systematic mapping study in microservice architecture , in: IEEE 9th International Conference on Service-Oriented Computing and Applications, IEEE, 2016, pp. 44–51.Google Scholar - [63] , A workflow language for research e-infrastructures, Int. J. Data Sci. Anal. 11 (4) (2021) 361–376.Google Scholar
- [64] DAGman: The directed acyclic graph manager, http://www.cs.wisc.edu/condor/dagman.Google Scholar
- [65] Common workflow language specifications, v1.0.2, 2020, https://www.commonwl.org/v1.0/. (Accessed April 2020).Google Scholar
- [66] , Grid service orchestration using the business process execution language (BPEL), J. Grid Comput. 3 (3) (2005) 283–304.Google Scholar
- [67] , A comparison of using Taverna and BPEL in building scientific workflows: The case of caGrid, Concurr. Comput.: Pract. Exper. 22 (9) (2010) 1098–1117.Google Scholar
- [68] ,
BPEL4Job: A fault-handling design for job flow management , in: International Conference on Service-Oriented Computing, Springer Berlin Heidelberg, 2007, pp. 27–42.Google Scholar - [69] Amazon simple workflow service, 2022, https://docs.aws.amazon.com/amazonswf/latest/developerguide/swf-welcome.html. (Accessed January 2022).Google Scholar
- [70] GitHub actions, 2022, https://github.com/features/actions/. (Accessed January 2022).Google Scholar
- [71] AWS CodePipeline, 2022, https://aws.amazon.com/codepipeline/. (Accessed January 2022).Google Scholar
- [72] , The many faces of publish/subscribe, ACM Comput. Surv. 35 (2) (2003) 114–131.Google ScholarDigital Library
- [73] A. Alqaoud, et al., Publish/subscribe as a model for scientific workflow interoperability, in: 4th Workshop on Workflows in Support of Large-Scale Science, 2009, pp. 1–10.Google Scholar
- [74] , A framework for real time processing of sensor data in the cloud, J. Sensors 2015 (2015).Google Scholar
- [75] ,
Online decision-making using edge resources for content-driven stream processing , in: 13th International Conference on e-Science, IEEE, 2017, pp. 384–392.Google Scholar - [76] Experimental Physics and Industrial Control System (EPICS), 2022, https://epics.anl.gov. (Accessed August 2022).Google Scholar
- [77] M. Quigley, et al., ROS: An open-source Robot Operating System, in: ICRA Workshop on Open Source Software, Vol. 3, 2009, p. 5.Google Scholar
- [78] , iRODS primer 2: Integrated Rule-Oriented Data System, Synth. Lect. Inf. Concepts Retr. Serv. 9 (3) (2017) 1–131.Google Scholar
- [79] B. Ur, et al., Practical trigger-action programming in the smart home, in: Conference on Human Factors in Computing Systems, 2014, pp. 803–812.Google Scholar
- [80] B. Ur, et al., Trigger-action programming in the wild: An analysis of 200,000 IFTTT recipes, in: Conference on Human Factors in Computing Systems, 2016, pp. 3227–3231.Google Scholar
- [81] ,
High-throughput neuroanatomy and trigger-action programming: A case study in research automation , in: 1st International Workshop on Autonomous Infrastructure for Science, 2018,10.1145/3217197.3217206.Google ScholarDigital Library - [82] , The Multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: Applications in neuroscience and neuroinformatics research, Front. Neuroinform. 8 (2014) 30.Google Scholar
- [83] , CASA and LEAD: Adaptive cyberinfrastructure for real-time multiscale weather forecasting, Computer 39 (11) (2006) 56–64.Google Scholar
- [84] ,
Where’s the bear?–Automating wildlife image processing using IoT and edge cloud systems , in: IEEE/ACM Second International Conference on Internet-of-Things Design and Implementation, IEEE, 2017, pp. 247–258.Google Scholar - [85] ,
SPRUCE: A system for supporting urgent high-performance computing , in: Grid-Based Problem Solving Environments, Springer, 2007, pp. 295–311.Google Scholar - [86] ,
Using dynamic data driven cyberinfrastructure for next generation disaster intelligence , in: International Conference on Dynamic Data Driven Application Systems, Springer, 2020, pp. 18–21.Google Scholar - [87] , Dynamic distribution of high-rate data processing from CERN to remote HPC data centers, Comput. Softw. Big Sci. 5 (1) (2021) 1–13.Google Scholar
- [88] , TeraGrid science gateways and their impact on science, Computer 41 (11) (2008) 32–41.Google ScholarDigital Library
- [89] , Real-time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis, 2021, arXiv:2106.11469.Google Scholar
- [90] ,
NEWT: A RESTful service for building high performance computing web applications , in: Gateway Computing Environments Workshop, IEEE, 2010, pp. 1–11.Google Scholar - [91] ,
Tapis: An API platform for reproducible, distributed computational research , in: Future of Information and Communication Conference, Springer, 2021, pp. 878–900.Google Scholar - [92] , Distributed computing in practice: The condor experience, Concurr. Comput.: Pract. Exper. 17 (2–4) (2005) 323–356.Google Scholar
- [93] ,
Balsam: Near real-time experimental data analysis on supercomputers , in: 1st IEEE/ACM Workshop on Large-Scale Experiment-in-the-Loop Computing, IEEE, 2019, pp. 26–31.Google Scholar - [94] , Towards accommodating real-time jobs on HPC platforms, 2021, https://arxiv.org/abs/2103.13130.Google Scholar
- [95] ,
Enabling discovery data science through cross-facility workflows , in: IEEE International Conference on Big Data, 2021, pp. 3671–3680, 10.1109/BigData52589.2021.9671421.Google Scholar - [96] , The LBNL Superfacility Project Report, 2022,10.48550/arXiv.2206.11992.Google Scholar
- [97] ,
Automation for data-driven research with the NERSC superfacility API , in: High Performance Computing, Springer International Publishing, Cham, 2021, pp. 333–345.Google Scholar - [98] ,
DataFed: Towards reproducible research via federated data management , in: International Conference on Computational Science and Computational Intelligence, IEEE, 2019, pp. 1312–1317.Google Scholar - [99] , Towards robot scientists for autonomous scientific discovery, Automated Experimentation 2 (1) (2010) 1–11.Google Scholar
- [100] , ChemOS: Orchestrating autonomous experimentation, Science Robotics 3 (19) (2018) eaat5559.Google Scholar
- [101] , Organic synthesis in a modular robotic system driven by a chemical programming language, Science 363 (6423) (2019).Google Scholar
- [102] , A mobile robotic chemist, Nature 583 (7815) (2020) 237–241.Google Scholar
- [103] , Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities, Nat. Rev. Phys. 3 (10) (2021) 685–697.Google Scholar
Index Terms
(auto-classified)Globus automation services: Research process automation across the space–time continuum
Comments