SC22 Proceedings

The International Conference for High Performance Computing, Networking, Storage, and Analysis

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Containerized Bioinformatics Ecosystem for HPC

Workshop: HUST-22: 9th International Workshop on HPC User Support Tools

Authors: Yucheng Zhang, Lev Gorenstein, Payas Bhutra, and Ryan DeRue (Purdue University)

Abstract: In High-performance computing (HPC) environments, SingularityCE has been widely used, and the primary reason for its popularity is that it can significantly reduce system administrators’ work of deploying applications. Traditionally, HPC administrators may need thousands of hours to deploy a broad stack of bioinformatics applications. SingularityCE has the potential to transform traditional methods of installing and managing applications. We introduce how our HPC center used SingularityCE to deploy about 600 containerized bioinformatics applications, which were tested by staff with expertise in bioinformatics , onto 7 production systems. This presentation also explores how, leveraging LMOD, containerization was made transparent to users through environment modules for these container images. Finally, it discusses how we deployed applications with graphical user interface to Open OnDemand as interactive applications, and how we modified python-based containers to support Jupyter Notebook. The sum of these contributions provides a robust and reproducible computing ecosystem for life science researchers.


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