HPC Extensions to the OpenKIM Processing Pipeline

Daniel S Karls; Steven M. Clark; Brendon A. Waters; Ryan S Elliott; Ellad B. Tadmor

doi:10.1109/eScience55777.2022.00041

HPC Extensions to the OpenKIM Processing Pipeline

Daniel S Karls
, Steven M. Clark
, Brendon A. Waters
, Ryan S Elliott
, Ellad B. Tadmor

Aerospace Engineering and Mechanics

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

3 Scopus citations

Abstract

The Open Knowledgebase of Interatomic Models (OpenKIM) is an NSF Science Gateway that archives fully functional computer implementations of interatomic models (potentials and force fields) and simulation codes that use them to compute material properties. Interatomic models are coupled with compatible simulation codes and executed in a fully automated manner by the OpenKIM processing pipeline, a cloud-based computation platform. The pipeline as previously introduced in the literature was insufficient to support the large volume and scale of computations that have become necessary within the materials science community. Accordingly, we present extensions made to the pipeline that allow it to utilize High-Performance Computing (HPC) resources in an efficient and performant fashion.

Original language	English (US)
Title of host publication	Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	278-283
Number of pages	6
ISBN (Electronic)	9781665461245
DOIs	https://doi.org/10.1109/eScience55777.2022.00041
State	Published - 2022
Event	18th IEEE International Conference on e-Science, eScience 2022 - Salt Lake City, United States Duration: Oct 10 2022 → Oct 14 2022

Publication series

Name	Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022

Conference

Conference	18th IEEE International Conference on e-Science, eScience 2022
Country/Territory	United States
City	Salt Lake City
Period	10/10/22 → 10/14/22

Bibliographical note

Funding Information:
The authors wish to acknowledge support from the Science Gateways Community Institute (SGCI) [3]. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE) [4], which is supported by National Science Foundation grant number ACI-1548562. Specifically, this work used the Stampede2 cluster at the Texas Advanced Computing Center (TACC) and Jetstream [25] services hosted at Indiana University and TACC through allocation TG-MAT200008. Finally, we are grateful to XSEDE for enabling S. M. Clark to work with us through the Extended Collaborative Support Service (ECSS) [26] program. This work is supported by the National Science Foundation under awards DMR-1834251 and DMR-1834332.

Funding Information:
This work is supported by the National Science Foundation under awards DMR-1834251 and DMR-1834332

Publisher Copyright:
© 2022 IEEE.

Keywords

cyberinfrastructure
high-performance computing
molecular dynamics

Publisher link

10.1109/eScience55777.2022.00041

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Karls, D. S., Clark, S. M., Waters, B. A., Elliott, R. S., & Tadmor, E. B. (2022). HPC Extensions to the OpenKIM Processing Pipeline. In Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022 (pp. 278-283). (Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/eScience55777.2022.00041

HPC Extensions to the OpenKIM Processing Pipeline. / Karls, Daniel S; Clark, Steven M.; Waters, Brendon A. et al.
Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022. Institute of Electrical and Electronics Engineers Inc., 2022. p. 278-283 (Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Karls, DS, Clark, SM, Waters, BA , Elliott, RS & Tadmor, EB 2022, HPC Extensions to the OpenKIM Processing Pipeline. in Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022. Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022, Institute of Electrical and Electronics Engineers Inc., pp. 278-283, 18th IEEE International Conference on e-Science, eScience 2022, Salt Lake City, United States, 10/10/22. https://doi.org/10.1109/eScience55777.2022.00041

Karls DS, Clark SM, Waters BA , Elliott RS , Tadmor EB. HPC Extensions to the OpenKIM Processing Pipeline. In Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022. Institute of Electrical and Electronics Engineers Inc. 2022. p. 278-283. (Proceedings - 2022 IEEE 18th International Conference on e-Science, eScience 2022). doi: 10.1109/eScience55777.2022.00041

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abstract = "The Open Knowledgebase of Interatomic Models (OpenKIM) is an NSF Science Gateway that archives fully functional computer implementations of interatomic models (potentials and force fields) and simulation codes that use them to compute material properties. Interatomic models are coupled with compatible simulation codes and executed in a fully automated manner by the OpenKIM processing pipeline, a cloud-based computation platform. The pipeline as previously introduced in the literature was insufficient to support the large volume and scale of computations that have become necessary within the materials science community. Accordingly, we present extensions made to the pipeline that allow it to utilize High-Performance Computing (HPC) resources in an efficient and performant fashion.",

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note = "Funding Information: The authors wish to acknowledge support from the Science Gateways Community Institute (SGCI) [3]. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE) [4], which is supported by National Science Foundation grant number ACI-1548562. Specifically, this work used the Stampede2 cluster at the Texas Advanced Computing Center (TACC) and Jetstream [25] services hosted at Indiana University and TACC through allocation TG-MAT200008. Finally, we are grateful to XSEDE for enabling S. M. Clark to work with us through the Extended Collaborative Support Service (ECSS) [26] program. This work is supported by the National Science Foundation under awards DMR-1834251 and DMR-1834332. Funding Information: This work is supported by the National Science Foundation under awards DMR-1834251 and DMR-1834332 Publisher Copyright: {\textcopyright} 2022 IEEE.; 18th IEEE International Conference on e-Science, eScience 2022 ; Conference date: 10-10-2022 Through 14-10-2022",

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HPC Extensions to the OpenKIM Processing Pipeline

Abstract

Publication series

Conference

Bibliographical note

Keywords

Publisher link

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