docker.md

Docker

• For Ubuntu, want to install docker-ce ("Community edition") rather than docker.io (a now-out-of-date version)

  The instructions are here.

  Ended up doing:

  sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu focal stable"
  sudo apt-get install docker-ce docker-ce-cli containerd.io
  

• To install docker for minecraft, I changed to the directory containing the Dockerfile in the miner package installation, and then followed the instructions in the miner book.

  cd ~/Rlibs/miner/Dockerfile .
  sudo docker build -t minecraft .
  

• To view the IP address of a docker container, type:

  ip addr show
  

  Look for lines following "docker"

• My slides about docker:

  • without notes
  • with notes
  • video of the lecture

• For r-devel with R/qtl, create a Dockerfile with:

  FROM rocker/r-devel
  RUN RD -e "install.packages('qtl')"
  

  and then do sudo docker build -t rdevel-qtl .

  That will create the image you want. Then run a container and open bash using:

  sudo docker run -it rdevel-qtl bash

  To install a package from github, use the remotes package.

  Also note: with rocker/r-devel, you start R using RD.

• To use R-devel with the clang compiler and UBsan (undefined behavior checker), use FROM rocker/r-devel-ubsan-clang. You again need to use RD within the container to run R, and also need docker run --cap-add SYS_PTRACE.

  So once you've created the container (with say sudo docker build -t rdevel-clang-ubsan .), you run it with:

  sudo docker run --cap-add SYS_PTRACE -it rdevel-clang-ubsan bash

• View images

  sudo docker images
  sudo docker image ls
  

• View running containers

  sudo docker container ls -a
  

• Start a container in interactive mode

  sudo docker start -i [container_name]
  

• Run a container from an image, interactively in a bash shell

  sudo docker run -it [image_name] bash
  

• Remove a running container

  sudo docker rm [container_name]
  

• Remove an image

  sudo docker image rm [repository or image id]