HPC:Singularity

Singularity

Singularity is an open-source application for creating and running software containers, designed primarily for scientific computing on Linux-based computing clusters like the Penn Medicine HPC system. Singularity containers enable self-contained, stable, portable, and reproducible computing environments and software stacks that can be shared and used across different machines and computing clusters, such as for research collaborations spanning multiple institutions.

Usage

Begin by launching an interactive/non-interactive session (bsub -Is bash). Singularity is installed on all HPC nodes outside of the environment module system, so there is no need to load a module in order to use it. Instead, you can directly use the singularity commands.

Note: commands that require sudo will not be available to you on HPC systems. The current version of Singularity installed is 3.7.1.

For detailed help information run 'singularity help' within an interactive session.