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DOCKER

Installation for Ubuntu

More information can be found on the "engine install ubuntu".

# Add Docker's official GPG key:
sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc

# Add the repository to Apt sources:
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update

# Install the latest version
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

More information can be found on the linux postinstall.

# Create the `docker` group. The Docker group already exists, so there is no need to run this command.
sudo groupadd docker

# Add your user to the docker group.
sudo usermod -aG docker $USER

# Activate the changes to groups. 
# I think it is better to restart the system than to run this command. I encountered a weird issue when I installed Docker Compose.
newgrp docker

# Verify docker
docker run hello-world

Uninstall Docker Engine

More information can be found on the official website.

sudo apt-get purge docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin docker-ce-rootless-extras

sudo rm -rf /var/lib/docker
sudo rm -rf /var/lib/containerd

sudo rm /etc/apt/sources.list.d/docker.list
sudo rm /etc/apt/keyrings/docker.asc

Basic Commands

Here's a guide to essential Docker commands, followed by a cheat sheet for quick reference.

Listing Docker Images and Containers

List Images:

To view all Docker images on your system:

docker images

This displays a table of images with details like repository, tag, and image ID.

List Running Containers:

To see all currently running containers:

docker ps

This shows a list of active containers with their IDs, names, and statuses.

List All Containers

To list all containers, including those that are stopped:

bash docker ps -a This provides a comprehensive list of all containers, regardless of their state.

Managing Docker Images

Pull an Image

To download an image from Docker Hub:

docker pull <image_name>

Replace <image_name> with the desired image, e.g., ubuntu.

Remove an Image

To delete a specific image:

docker rmi <image_name_or_id>

Use the image name or ID from the docker images list.

Building Docker Images

Build an Image from a Dockerfile

To create a Docker image from a Dockerfile:

docker build -t <image_name> <path_to_dockerfile_directory>

Replace <image_name> with your desired image name and <path_to_dockerfile_directory> with the path to the directory containing your Dockerfile. The -t flag tags the image with a name.

Example:

docker build -t myapp:latest .

This builds an image named myapp with the tag latest from the Dockerfile in the current directory.

Running and Managing Containers

Run a Container

To create and start a new container:

docker run [OPTIONS] <image_name>

Common options include: - -d: Run the container in detached mode (in the background). - -it: Run the container in interactive mode with a terminal. - --name <container_name>: Assign a name to the container. - -p <host_port>:<container_port>: Map host port to container port. - -v <host_directory>:<container_directory>: Mount a host directory as a volume in the container.

Example:

docker run -it bird-behavior bash

Example:

This runs a container named bird-behavior and opens an interactive bash shell inside the bird-behavior container.

docker run -d -p 8080:80 -v /host/data:/container/data --name mynginx nginx

This runs an Nginx container named mynginx in detached mode, mapping port 8080 on the host to port 80 in the container, and mounts the host directory /host/data to /container/data in the container.

Resource constraints: For more details check here.

docker run --cpus="4" --memory="8g" ...

Execute Commands in a Running Container

To run a command inside a running container:

docker exec [OPTIONS] <container_name_or_id> <command>
 ```

Common options:
- `-it`: Run in interactive mode with a terminal.

Example:

```bash
docker exec -it mynginx /bin/bash

This opens an interactive bash shell inside the mynginx container.

Stop a Running Container

To stop a container:

docker stop <container_name_or_id>

Start a Stopped Container

To start a container that has been stopped:

docker start <container_name_or_id>

Remove a Container

To delete a container:

docker rm <container_name_or_id>

Note: Ensure the container is stopped before removing it.

Viewing Logs and Inspecting Containers

View Container Logs

To see the logs of a container:

docker logs <container_name_or_id>

Inspect Container Details

To get detailed information about a container:

docker inspect <container_name_or_id>

Docker Compose

Docker Compose is a tool that simplifies running applications with multiple containers. By defining services, networks, and volumes in a single YAML file, you can start and manage all components of your application with one command.

You can find an example of a Docker Compose file here. The description is provided below.

Creating a docker-compose.yml File

Create a docker-compose.yml file with the following content:

version: '3'
services:
  jekyll:
    image: jekyll/jekyll:latest
    command: jekyll serve --watch --incremental
    ports:
      - "4000:4000"
    volumes:
      - .:/srv/jekyll

Running the Docker Compose File

To start the services defined in your docker-compose.yml file, run:

docker-compose up

Cheat Sheet

Command Description
docker images List all Docker images
docker ps List running containers
docker ps -a List all containers (running and stopped)
docker pull <image_name> Pull an image from Docker Hub
docker rmi <image_name_or_id> Remove a Docker image
docker build -t <image_name> <path> Build an image from a Dockerfile
docker run [OPTIONS] <image_name> Run a new container
docker exec [OPTIONS] <container> <command> Execute a command in a running container
docker stop <container_name_or_id> Stop a running container
docker start <container_name_or_id> Start a stopped container
docker rm <container_name_or_id> Remove a container
docker logs <container_name_or_id> View logs of a container
docker inspect <container_name_or_id> Inspect detailed information of a container

Apptainer

In Snellius, there is Apptainer instead of Docker.

Apptainer (formerly Singularity) is a containerization tool designed for high-performance computing (HPC), scientific workloads, and secure application deployment. Unlike Docker, Apptainer focuses on security, reproducibility, and portability, allowing users to run containers without requiring root privileges. It uses single-file SIF (Singularity Image Format) images, making it ideal for environments like HPC clusters and supercomputers.

The equivalent commands for the Docker commands you mentioned are:

| Command | Description | | apptainer cache list | docker images | | apptainer instance list | docker ps -a | | apptainer cache clean | docker rmi imageid. See example below. | | docker rm containerid | apptainer instance stop <instance_name> |

These directories store the downloaded images.

ls ~/.apptainer/cache/library
ls ~/.apptainer/cache/oci-tmp

E.g. If you pulled docker using apptainer pull, it should have been saved as a .sif file in your working directory 

apptainer pull docker://godlovedc/lolcow 
apptainer inspect lolcow_latest.sif
# Since Apptainer doesn’t use a centralized image store like Docker, you typically just remove the .sif file:
rm lolcow_latest.sif
# If you want to clean the cache (which includes OCI blobs and temporary files), use:
apptainer cache clean