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Empowering Scientific Discovery Through Computing at the Advanced Photon Source

Published: 12 November 2023 Publication History

Abstract

This paper explores the challenges and solutions for managing and processing the vast amount of data generated by the Advanced Photon Source (APS), a synchrotron light source facility producing ultra-bright x-rays for diverse scientific domains. With 68 experimental beamlines covering materials research, biology, and more, the APS serves a wide user base across academia, government, and industry. The ongoing upgrade of the APS storage ring and installation of new instruments will amplify data generation and processing demands. This paper discusses the approach to address these demands through automated data processing using standardized workflows that produce faster scientific insights. The APS Data Management System coordinates various data related tasks to manage storage, data transfer, metadata cataloging, data processing, and interfaces with tools provided by Globus. Through integration with the Argonne Leadership Computing Facility (ALCF), APS users can efficiently access high-performance computing resources. Standardized workflows have led to reduced computational burdens on scientists and greater accessibility of high performance computing resources. We demonstrate how standardization and collaboration enable scientists to rapidly convert raw data into meaningful scientific results, establishing a streamlined path from data collection to analysis and ultimately to publication.

References

[1]
Office of Science and Technology Policy (OSTP) 2022. Ensuring Free, Immediate, and Equitable Access to Federally Funded Research. Office of Science and Technology Policy (OSTP). https://www.whitehouse.gov/wp-content/uploads/2022/08/08-2022-OSTP-Public-Access-Memo.pdf
[2]
Argonne National Laboratory 2023. The ALCF Community Data Coop. Argonne National Laboratory. https://acdc.alcf.anl.gov
[3]
Argonne National Laboratory 2023. The Argonne Leadership Computing Facility (ALCF). Argonne National Laboratory. https://www.alcf.anl.gov
[4]
Argonne National Laboratory 2023. The Aurora Supercomputer. Argonne National Laboratory. https://www.alcf.anl.gov/aurora
[5]
Argonne National Laboratory 2023. COLD for Processing Laue Diffraction Images Collected with Coded-Apertures. Argonne National Laboratory. https://cold.readthedocs.io/en/latest
[6]
Argonne National Laboratory 2023. eBERLight. Argonne National Laboratory. https://sbc.aps.anl.gov
[7]
National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility 2023. National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility (GMCA). National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility. https://www.gmca.aps.anl.gov
[8]
Argonne National Laboratory 2023. The Polaris Supercomputer. Argonne National Laboratory. https://www.alcf.anl.gov/polaris
[9]
Argonne National Laboratory 2023. TomoEncoders. Argonne National Laboratory. https://tomoencoders.readthedocs.io
[10]
Daniel Allan, Thomas Caswell, Stuart Campbell, and Maksim Rakitin. 2019. Bluesky’s Ahead: A Multi-Facility Collaboration for an a la Carte Software Project for Data Acquisition and Management. Synchrotron Radiation News 32, 3 (2019), 19–22. https://doi.org/10.1080/08940886.2019.1608121 arXiv:https://doi.org/10.1080/08940886.2019.1608121
[11]
Bryce Allen, John Bresnahan, Lisa Childers, Ian Foster, Gopi Kandaswamy, Raj Kettimuthu, Jack Kordas, Mike Link, Stuart Martin, Karl Pickett, and Steven Tuecke. 2012. Software as a Service for Data Scientists. Commun. ACM 55, 2 (feb 2012), 81–88. https://doi.org/10.1145/2076450.2076468
[12]
M. Borland 2018. The Upgrade of the Advanced Photon Source. In Proc. 9th International Particle Accelerator Conference (IPAC’18), Vancouver, BC, Canada, April 29-May 4, 2018(International Particle Accelerator Conference, 9). JACoW Publishing, Geneva, Switzerland, 2872–2877. https://doi.org/10.18429/JACoW-IPAC2018-THXGBD1 https://doi.org/10.18429/JACoW-IPAC2018-THXGBD1.
[13]
Miaoqi Chu. 2023. boost_corr. Argonne National Laboratory. https://github.com/AdvancedPhotonSource/boost_corr
[14]
Ian Foster. 2011. Globus Online: Accelerating and Democratizing Science through Cloud-Based Services. IEEE Internet Computing 15, 3 (2011), 70–73. https://doi.org/10.1109/MIC.2011.64
[15]
Barbara Frosik. 2023. cohere. Argonne National Laboratory. https://cohere.readthedocs.io/en/latest/about.html
[16]
Arthur Glowacki. 2023. XRF Maps. Argonne National Laboratory. https://github.com/AdvancedPhotonSource/XRF-Maps/blob/master/README.md
[17]
John Hammonds. 2023. rsMap3D. Argonne National Laboratory. https://github.com/AdvancedPhotonSource/rsMap3D
[18]
Steven Henke. 2023. Ptychodus. Argonne National Laboratory. https://github.com/AdvancedPhotonSource/ptychodus
[19]
Zhengchun Liu, Ahsan Ali, Peter Kenesei, Antonino Miceli, Hemant Sharma, Nicholas Schwarz, Dennis Trujillo, Hyunseung Yoo, Ryan Coffee, Naoufal Layad, Jana Thayer, Ryan Herbst, Chunhong Yoon, and Ian Foster. 2021. Bridging Data Center AI Systems with Edge Computing for Actionable Information Retrieval. In 2021 3rd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP). IEEE, St. Louis, MO, 15–23. https://doi.org/10.1109/XLOOP54565.2021.00008
[20]
Zhengchun Liu, Tekin Bicer, Rajkumar Kettimuthu, and Ian Foster. 2019. Deep Learning Accelerated Light Source Experiments. In 2019 IEEE/ACM Third Workshop on Deep Learning on Supercomputers (DLS). 20–28. https://doi.org/10.1109/DLS49591.2019.00008
[21]
Zhengchun Liu, Tekin Bicer, Rajkumar Kettimuthu, Doga Gursoy, Francesco De Carlo, and Ian Foster. 2020. TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion. J. Opt. Soc. Am. A 37, 3 (Mar 2020), 422–434. https://doi.org/10.1364/JOSAA.375595
[22]
Viktor Nikitin. 2023. TomocuPy – efficient GPU-based tomographic reconstruction with asynchronous data processing. Journal of Synchrotron Radiation 30, 1 (Jan 2023), 179–191. https://doi.org/10.1107/S1600577522010311
[23]
Nicholas Schwarz. 2022. The APS Scientific Computing Strategy. Technical Report. Argonne National Laboratory. https://www.aps.anl.gov/files/APS-Uploads/XSD/XSD-Strategic-Plans/APSScientificComputingStrategy-2022-12-09-FINAL.pdf
[24]
Nicholas Schwarz, Stuart Campbell, Alexander Hexemer, Apurva Mehta, and Jana Thayer. 2020. Enabling Scientific Discovery at Next-Generation Light Sources with Advanced AI and HPC. In Driving Scientific and Engineering Discoveries Through the Convergence of HPC, Big Data and AI, Jeffrey Nichols, Becky Verastegui, Arthur ‘Barney’ Maccabe, Oscar Hernandez, Suzanne Parete-Koon, and Theresa Ahearn (Eds.). Springer International Publishing, Cham, 145–156.
[25]
Brian H. Toby and Robert B. Von Dreele. 2013. GSAS-II: the genesis of a modern open-source all purpose crystallography software package. Journal of Applied Crystallography 46, 2 (Apr 2013), 544–549. https://doi.org/10.1107/S0021889813003531
[26]
Rafael Vescovi, Ryan Chard, Nickolaus D. Saint, Ben Blaiszik, Jim Pruyne, Tekin Bicer, Alex Lavens, Zhengchun Liu, Michael E. Papka, Suresh Narayanan, Nicholas Schwarz, Kyle Chard, and Ian T. Foster. 2022. Linking scientific instruments and computation: Patterns, technologies, and experiences. Patterns 3, 10 (2022), 100606. https://doi.org/10.1016/j.patter.2022.100606
[27]
Siniša Veseli, Nicholas Schwarz, and Collin Schmitz. 2018. APS Data Management System. Journal of Synchrotron Radiation 25, 5 (Sep 2018), 1574–1580. https://doi.org/10.1107/S1600577518010056

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          cover image ACM Other conferences
          SC-W '23: Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis
          November 2023
          2180 pages
          ISBN:9798400707858
          DOI:10.1145/3624062
          Publication rights licensed to ACM. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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          Published: 12 November 2023

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          Author Tags

          1. Computing
          2. Data Management
          3. Research
          4. Software
          5. Workflows

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