Sandbox containers

Container basics

 

For how to use Singularity/Apptainer containers please see our course at: http://wally-head.unil.ch/courses/r_python_singularity/#/

Sandboxes

A container image (the .sif file) is read only and its contents cannot be changed which makes them perfect for distributing safe in the knowledge that they should run exactly as they were created.

Sometimes, especially when developing things, it's very useful to be able to interactively modify a container and this is what sandboxes are for.

Please be aware that anything done by hand is not reproducible so all steps should be transferred to the container definition file.

 

Creating and modifying a sandbox

 

Note that the steps here should be run on the cluster login node (curnagl.dcsr.unil.ch) as it is currently the only machine with the configuration in place to allow containers to be built.

To start you need a basic definition file - this can be an empty OS or something more complicated that already has some configuration.

In the following example we will use a definition that installs the latest version of R. We will then try and install extra packages before creating the immutable SIF image.

 

BootStrap: docker
From: ubuntu:20.04

%post
  apt update
  apt install -y locales gnupg-agent
  sed -i '/^#.* en_.*.UTF-8 /s/^#//' /etc/locale.gen
  sed -i '/^#.* fr_.*.UTF-8 /s/^#//' /etc/locale.gen
  locale-gen

  # install two helper packages we need
  apt install -y --no-install-recommends software-properties-common dirmngr

  # add the signing key (by Michael Rutter) for these repos
  wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
  
  apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 51716619E084DAB9

  # add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
  add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

  apt install -y --no-install-recommends r-base