Software

Modules and Bioinformatics Software

Unlike previous systems, a limited and generic set of software modules are maintained by NERSC and available for JGI users on Cori. Users should themselves build and maintain any more specialized software they may need.

Alternatives to using NERSC-provided software modules are:

  • Shifter, with the software built inside a Docker container
  • Anaconda virtual environments
  • A wide array of powerful compilers and tools are available to build software from source code. While scratch space is subject to NERSC's purge policy, many groups possess a "sandbox" allocation which is equally performant to $BSCRATCH, and shared among group members. (Running software from $HOME is strongly discouraged.)

Shifter

Shifter is a Docker-like software tool used to run containers on NERSC systems. More information on Shifter is available here, and Shifter training slides are also available. The main advantages of using Shifter are:

  • Using containers makes your workflow portable between Cori, other HPC facilities and clusters, and cloud resources
  • You no longer need to depend on system features, such as specific compiler versions, software libraries, or other tools
  • Because Shifter uses Docker containers, you can build and debug containers on your laptop or desktop, then be confident they will run the same way on Cori or other platforms.
  • Shifter exists because Docker does not incorporate the security requirements of a HPC facility. Docker requires an access model and permissions which are too broad; anyone who can run a container has access to the entire machine. Shifter implements a subset of the same functionality that Docker provides and can run Docker containers unmodified.

The process for building a container and running it with Shifter is roughly as follows:

  1. use Docker on a laptop or desktop machine to build a Docker container for your software
  2. push that container to Dockerhub or another Docker container registry and use Shifter on Cori to pull that image to the NERSC Shifter registry
  3. use Shifter on a batch node to run that container, and perform useful work

Note

The JGI has a containerization project, intended to provide standardized containers for the majority of JGI use-cases. If you need a container for a tool or pipeline, check with your consultants - you may find it's already been done for you. Documentation for the containerization project will be made available soon.

Anaconda

Anaconda virtual environments allow you to install software in a clean and reproducible manner. See this the training page for more information about using Anaconda at NERSC. Note that while Anaconda started life as a Python package manager, now R, Perl and many other computing languages and associated modules can also be installed using it. For more information about using Python at NERSC, please see our Python documentation.