Docker

Installing Docker
- Ubuntu installation (July 2020)
- Fedora installation (January 2020)
Getting Docker Images
Running Containers
- Interacting with containers
Listing Containers in Docker
Clearing Non-running Containers
Mounting a Host Filesystem
- Fix for permissions issues
Mapping Network Ports
Creating a Docker Image
- Interactively from an existing image
- Using a docker file
Docker Compose

Installing Docker

Installation steps have changed quite frequently with new releases of Docker. I will do my best to keep this up-to date, but no guarantees.

Ubuntu installation (July 2020)

Older versions of Docker were called docker, docker.io, or docker-engine. Now, the packages to install are docker-ce, docker-ce-cli, and containerd.io.

Official documentation:

https://docs.docker.com/engine/install/ubuntu/

For Ubuntu 20.04, follow instructions here.

Fedora installation (January 2020)

sudo dnf install docker
sudo sudo systemctl enable docker.service
sudo systemctl start docker.service

Note: Fedora 31 had problems starting the docker daemon.

Debugging with: sudo dockerd --debug shows “Devices cgroup isn’t mounted”. The solution was to modify the grub in order to start cgroup

sudo dnf install -y grubby
sudo grubby --update-kernel=ALL --args="systemd.unified_cgroup_hierarchy=0"

Reboot computer.

Finally, add user to the Docker group:

sudo groupadd docker && sudo gpasswd -a ${USER} docker

Log out and in again to see changes.

Getting Docker Images

Pull from Docker Hub:

docker pull hub.docker.com/r/microsoft/powershell

We may need to specify a tag, e.g.:

docker pull ouchc/relion3.1:ubuntu16.04

Search for images: docker search

See installed images: docker images

Running Containers

Use docker run to initially run a container.

Common options:

-d: run in background (daemonize)
-i: interactive
-t: tty
-p: make a port available outside container ple as:

FROM fedora:latest CMD env

Docker file reference: https://docs.docker.com/engine/reference/builder/

Best practices: https://docs.docker.com/develop/develop-images/dockerfile_best-practices/

In a directory with a Dockerfile run:

sudo docker build -t “my-image” .

If the build is successful you can see my-image in docker images output. Docker Compose

https://docs.docker.com/compose/

https://developer.fedoraproject.org/tools/docker/compose.html

Docker Compose is a tool to orchestrate Docker containers using a simple YAML file which describes your whole setup.

sudo dnf install docker-compose

–name: assign container a name
–rm: remove container when it exits

Interacting with containers

Once a container is running, you can easily start or stop it.

Start a container (can use an assigned name): docker start

Stop a container docker stop

Execute a command off a running container: docker exec

Look inside container: docker logs

Listing Containers in Docker

To show only running containers use:

docker container ls

The old, shorter way of doing this is docker ps.

Options:

-a: see all containers
-s: see container sizes

Clearing Non-running Containers

Containers that are not running are not taking any system resources besides disk space.

The docker run flag --rm will automatically remove a container when it exits.

Remove a specific container: docker rm 3e552code34a

Removes all stopped containers: docker container prune

Clean unused containers, networks, images, and volumes: docker system prune

Mounting a Host Filesystem

Use the -v flag:

docker run -v /host/directory:/container/directory -other -options image_name command_to_run

Fix for permissions issues

In Fedora, SELinux can cause issues with mounting volumes. The solution is to issue a SELinux rule: chcon -Rt svirt_sandbox_file_t /path/to/volume

This got easier recently since Docker finally merged a patch in docker-1.7.

This patch adds support for “z” and “Z” as options on the volume mounts (-v).

For example:

docker run -v /var/db:/var/db:z rhel7 /bin/sh

Will automatically do the chcon -Rt svirt_sandbox_file_t /var/db.

Even better, you can use Z.

docker run -v /var/db:/var/db:Z rhel7 /bin/sh

This will label the content inside the container with the exact MCS label that the container will run with, basically it runs chcon -Rt svirt_sandbox_file_t -l s0:c1,c2 /var/db, where s0:c1,c2 differs for each container.

For more info: https://docs.docker.com/storage/volumes/

e.g. to run my powershell docker container with a mounted home directory:

docker run -v /home/ravila/:/home/ravila/:Z -it mcr.microsoft.com/powershell

Mapping Network Ports

docker run --name mycontainer -p 8080:8080 -p 8000:8000

Creating a Docker Image

Interactively from an existing image

If you change anything (like install new packages) in the running container and exit the container the changes are not automatically saved. If you want to save them in an image, use docker commit.

Using a docker file

A Dockerfile content can be as simple as:

FROM fedora:latest
CMD env