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The HPC Container Experience on the Summit Supercomputer

Published:10 September 2023Publication History

ABSTRACT

Containers are seeing widespread use in the world of High Performance Computing, with many HPC Centers either providing their own containerization solution or adopting existing ones like Singularity and Apptainer. The demand for containerization options come from users who want to take advantage of the portability and reproducibility containers can provide, as well as being able to build and use applications that are only distributed in container form or are otherwise unsuited to natively run in an HPC environment. The users served by the Oak Ridge Leadership Computing Facility are no exception. We go over the past and current containerization offerings at the Oak Ridge Leadership Computing Facility, mainly focusing on the Summit supercomputer. We arrive at using a combination of Podman and Singularity to allow users to build and run containers directly on Summit, without requiring external resources or hardware for any step of the process. We look at a couple of projects running on Summit that greatly benefited from being able to use containers on Summit. And we compare benchmarks running natively and in containers on Summit at different scales, observing minimal performance difference and consistent behavior across all tests.

References

  1. [n. d.]. Containers on Summit — OLCF User Documentation. https://docs.olcf.ornl.gov/software/containers_on_summit.htmlGoogle ScholarGoogle Scholar
  2. [n. d.]. Fakeroot feature — SingularityCE User Guide 3.11 documentation. https://docs.sylabs.io/guides/3.11/user-guide/fakeroot.htmlGoogle ScholarGoogle Scholar
  3. [n. d.]. November 2022 | TOP500. https://top500.org/lists/top500/2022/11/Google ScholarGoogle Scholar
  4. [n. d.]. Overlay Filesystem — The Linux Kernel documentation. https://www.kernel.org/doc/html/latest/filesystems/overlayfs.htmlGoogle ScholarGoogle Scholar
  5. [n. d.]. Overview — NVIDIA Cloud Native documentation. https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/overview.htmlGoogle ScholarGoogle Scholar
  6. [n. d.]. SingularityCE and MPI applications — SingularityCE User Guide 3.11 documentation. https://docs.sylabs.io/guides/3.11/user-guide/mpi.htmlGoogle ScholarGoogle Scholar
  7. 2023. AlphaFold. https://github.com/deepmind/alphafold original-date: 2021-06-17T14:06:06Z.Google ScholarGoogle Scholar
  8. 2023. olcfcontainers / olcfbaseimages · GitLab. https://code.ornl.gov/olcfcontainers/olcfbaseimagesGoogle ScholarGoogle Scholar
  9. 2023. open-ce/open-ce. https://github.com/open-ce/open-ce original-date: 2020-09-03T20:23:41Z.Google ScholarGoogle Scholar
  10. 2023. Raptor Computing Systems::Talos™ II Secure Workstation. https://www.raptorcs.com/TALOSII/Google ScholarGoogle Scholar
  11. M. Gao, M. Coletti, R.B. Davidson, R. Prout, S. Abraham, B. Hernandez, and A. Sedova. 2022. Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer. 206–215. https://doi.org/10.1109/IPDPSW55747.2022.00045Google ScholarGoogle Scholar
  12. M. Gao, P. Lund-Andersen, A. Morehead, S. Mahmud, C. Chen, X. Chen, N. Giri, R.S. Roy, F. Quadir, T.C. Effler, R. Prout, S. Abraham, W. Elwasif, N.Q. Haas, J. Skolnick, J. Cheng, and A. Sedova. 2021. High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. 46–57. https://doi.org/10.1109/MLHPC54614.2021.00010Google ScholarGoogle Scholar
  13. John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli, and Demis Hassabis. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596, 7873 (Aug. 2021), 583–589. https://doi.org/10.1038/s41586-021-03819-2 Number: 7873 Publisher: Nature Publishing Group.Google ScholarGoogle Scholar
  14. Gregory M Kurtzer, Vanessa Sochat, and Michael W Bauer. 2017. Singularity: Scientific containers for mobility of compute. PloS one 12, 5 (2017), e0177459.Google ScholarGoogle ScholarCross RefCross Ref
  15. Oleksandr Rudyy, Marta Garcia-Gasulla, Filippo Mantovani, Alfonso Santiago, Raül Sirvent, and Mariano Vázquez. 2019. Containers in HPC: A Scalability and Portability Study in Production Biological Simulations. In Proceedings of 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).Google ScholarGoogle ScholarCross RefCross Ref
  16. Adam Simpson, Jack Morrison, Adam Carlyle, and Matt Belhorn. 2023. olcf / container-builder (GitLab). https://code.ornl.gov/olcf/container-builderGoogle ScholarGoogle Scholar
  17. A. Torrez, T. Randles, and R. Priedhorsky. 2019. HPC Container Runtimes have Minimal or No Performance Impact. In 2019 IEEE/ACM International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC (CANOPIE-HPC). 37–42.Google ScholarGoogle Scholar
  18. Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. 2018. DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics. https://doi.org/10.1016/j.cpc.2018.03.016 Pages: 178–184 Publication Title: Computer Physics Communications Volume: 228 original-date: 2017-12-12T15:23:44Z.Google ScholarGoogle Scholar
  19. Andrew J Younge, Kevin Pedretti, Ryan E Grant, and Ron Brightwell. 2017. A Tale of Two Systems: Using Containers to Deploy HPC Applications on Supercomputers and Clouds. In Proceedings of the 2017 IEEE International Conference on Cloud Computing Technology and Science (CloudCom).Google ScholarGoogle ScholarCross RefCross Ref

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      • Published in

        cover image ACM Conferences
        PEARC '23: Practice and Experience in Advanced Research Computing
        July 2023
        519 pages
        ISBN:9781450399852
        DOI:10.1145/3569951

        Copyright © 2023 ACM

        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: 10 September 2023

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