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Software

Modules and Bioinformatics Software

Unlike on the now-retired Genepool system, very few NERSC software modules are available for JGI user software on Cori or Denovo. We encourage users to use alternatives wherever possible, which will be more maintainable and portable to other platforms.

Alternatives to using software modules are:

  • Shifter, with the software installed in a Docker container
  • Anaconda virtual environments
  • You are, as always, welcome to install and maintain any software you like on NERSC systems within your own user disk space. While scratch space is subject to NERSC's purge policy, many groups hold a "sandbox" space which is equally performant to $BSCRATCH and shared among group members. (Running software from $HOME is strongly discouraged.)

Shifter

Shifter is Docker-like software for running 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, across Cori, Denovo, Edison, and to 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 sure they will run the same way on Cori or other NERSC platforms.
  • Shifter exists because Docker cannot be safely run on NERSC machines. Docker requires too much access to the system, anyone who can run a container can essentially access 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 use Shifter on Cori, Edison or Denovo 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.