Setup Docker Fortran image for CI
Install Docker image: add
docker group and your username to this group, to avoid needing
sudo for every
addgroup docker adduser $(whoami) docker
then reboot (not just logout, an actual system restart)
Install Docker on your laptop (the example here is for a Linux laptop)
snap install docker
after this step,
sudo should no longer be required.
Try the Hello World images, which should auto-download and print a welcome message
docker run hello-world
Search for a desired image.
Consider those images listed as “official”.
You might need to widen your terminal to 155 columns or so to render properly.
ubuntu as it’s quite popular for Docker and in general.
docker search ubuntu
Get the desired image
docker pull ubuntu
Verify the images on your computer
ubuntu takes just under 100 MB to start.
Start the Docker container on your laptop
docker run -it ubuntu
- interactive session
Verify the version running, it will have a
# superuser prompt:
These commands are issued NOT from within the Docker container itself (open a new terminal)
where are containers stored:
docker info | grep "Root Dir"
How much space is Docker using altogether:
du -sh /var/snap/docker
- use previous command to find where your Docker stuff is
docker images -a
list containers (running and stopped):
docker ps -a
stop a Docker container:
docker stop container_name
start a Docker container:
docker start container_name
login to a running Docker container:
docker exec -it container_name bash
get container environment variables:
docker exec container_name env
cleanup unused containers
docker system prune
docker image rm ubuntu:19.04
Configure Docker image
CI and other online, server and computer resources) can use Docker images. You can make a Docker image setup with everything you need, which is useful if the setup is cumbersome. For research reproducability, a Docker image gives a known software state that should be usable for many years.
Interactive setup method tends to make the final image larger than using
So let’s start off by using a
Dockerfile as that helps maintain smaller images with repeatable builds.
The Docker container can be turned into a new image that is usable from CI or other suitable Docker host.
We do not claim this Dockerfile to be optimal. Please let us know of suggested improvements.
# based on https://github.com/naftulikay/docker-bionic-vm/blob/master/Dockerfile FROM ubuntu:18.04 ENV container=docker TERM=xterm LC_ALL=en_US LANGUAGE=en_US LANG=en_US.UTF-8 # stop some interactive prompts, also need "-yq" on apt-get ENV DEBIAN_FRONTEND=noninteractive # locale RUN apt-get update -q > /dev/null && \ apt-get install --no-install-recommends -yq apt-utils locales language-pack-en dialog > /dev/null && \ locale-gen $LANGUAGE $LANG # add sudo commmand RUN apt-get -yq install sudo > /dev/null # create and switch to a non-priviliged (but sudo-enabled) user, arbitrary name RUN echo "nonprivuser ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers RUN useradd --no-log-init --home-dir /home/nonprivuser --create-home --shell /bin/bash nonprivuser && adduser nonprivuser sudo USER nonprivuser WORKDIR /home/nonprivuser # Git/Curl -- don't disable recommends here or you won't have Certification Authority certificates and will fail RUN sudo apt-get install -yq git curl > /dev/null # packages specific to your needs RUN sudo apt-get install --no-install-recommends -yq make gfortran libcoarrays-dev libopenmpi-dev open-coarrays-bin > /dev/null && \ sudo apt-get clean -q # latest cmake RUN git clone --depth 1 https://github.com/scivision/cmake-utils && \ mkdir -v /home/nonprivuser/.local && \ cd cmake-utils && PREFIX=/home/nonprivuser/.local ./cmake_setup.sh > /dev/null && \ mv -v /home/nonprivuser/.local/cmake* /home/nonprivuser/.local/cmake ENV PATH=$PATH:/home/nonprivuser/.local/cmake/bin # other optional installs # RUN sudo apt-get install --no-install-recommends -yq octave
Create the file above named
Dockerfile in your Git repo.
Build the Docker image:
docker build -t opencoarrays_fortran .
assuming you’re in the same directory as
Check the image exists. For me it was about 350 MB:
Before committing for upload, you must invoke the container.
docker run opencoarrays_fortran
This will almost immediately start and stop, as you didn’t give it a command to run or persist.
Get the hexadecimal container ID by:
docker ps -a
the container will have an auto-assigned name like
Note the hexadecimal “container ID”.
upload Docker image
Once you have configured a Docker container on your laptop suitable for your purposes, you may wish to share this container and use it on other hosts such as CI. This can be done with DockerHub.
Once you are ready to upload the image, note the “container ID”, which is the hexadecimal number at the terminal prompt of the Docker container, under
The container hex ID must appear under
docker ps, just being in
docker images is not enough.
docker commit -m "basic fortran OpenCoarrays setup" hex_id dockerhub_username/opencoarrays_fortran
The changes to the image the container made are gathered into a new image. It may take a minute or two if your image is large. Ideally with a small image it will take only a couple seconds. The new image has not yet left your computer, it will show up under
Once uploaded, your Docker image is visible to the world by default.
Login to DockerHub
docker login -u dockerhub_username
Push (upload) this image to DockerHub. Note this image is world-visible by default!
docker push dockerhub_username/opencoarrays_fortran
If your image is very large > 1 GB, be aware it will take a while to upload, and for the CI system to download. This is a telltale that it’s important to keep Docker images small.
docker exec command is a new shell instance. So changing directories in one
docker exec has no effect on subsequent commands for example.