Self-Scaling Clusters and Reproducible Containers to Enable Scientific Computing

摘要

Container technologies such as Docker have become a crucial component of many software industry practices especially those pertaining to reproducibility and portability. The containerization philosophy has influenced the scientific computing community, which has begun to adopt - and even develop - container technologies (such as Singularity). Leveraging containers for scientific software often poses challenges distinct from those encountered in industry, and requires different methodologies. This is especially true for HPC. With an increasing number of options for HPC in the cloud (including NSF-funded cloud projects), there is strong motivation to seek solutions that provide flexibility to develop and deploy scientific software on a variety of computational infrastructures in a portable and reproducible way. The Cyberinfrastructure Resource Integration team in the XSEDE project has developed a simple tool which provides HPC infrastructure in the cloud that scales with user demand. We now present one possible solution which uses the Nix package manager in an MPI-capable Docker container that is converted to Singularity. It provides consistent installations, dependencies, and environments in each image that are reproducible and portable across scientific computing infrastructures. We demonstrate the utility of these containers with cluster benchmark runs in a self-scaling virtual cluster using the Slurm scheduler deployed in the Jetstream and Aristotle Red Cloud OpenStack clouds. We conclude that this technique is useful as a template for scientific software application containers to be used in the XSEDE compute environment, other Singularity HPC environments, and cloud computing environments.