Introducing Containers
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Almost all software depends on other software components to function, but these components have independent evolutionary paths.
Small environments that contain only the software that is needed for a given task are easier to replicate and maintain.
Critical systems that cannot be upgraded, due to cost, difficulty, etc. need to be reproduced on newer systems in a maintainable and self-documented way.
Virtualization allows multiple environments to run on a single computer.
Containerization improves upon the virtualization of whole computers by allowing efficient management of the host computer’s memory and storage resources.
Containers are built from ‘recipes’ that define the required set of software components and the instructions necessary to build/install them within a container image.
Docker is just one software platform that can create containers and the resources they use.
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Introducing the Docker Command Line
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A toolbar icon indicates that Docker is ready to use (on Windows and macOS).
You will typically interact with Docker using the command line.
To learn how to run a certain Docker command, we can type the command followed by the --help flag.
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Exploring and Running Containers
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The docker image pull command downloads Docker container images from the internet.
The docker image ls command lists Docker container images that are (now) on your computer.
The docker container run command creates running containers from container images and can run commands inside them.
When using the docker container run command, a container can run a default action (if it has one), a user specified action, or a shell to be used interactively.
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Cleaning Up Containers
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docker container has subcommands used to interact and manage containers.
docker image has subcommands used to interact and manage container images.
docker container ls or docker ps can provide information on currently running containers.
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Finding Containers on Docker Hub
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The Docker Hub is an online repository of container images.
Many Docker Hub container images are public, and may be officially endorsed.
Each Docker Hub page about a container image provides structured information and subheadings
Most Docker Hub pages about container images contain sections that provide examples of how to use those container images.
Many Docker Hub container images have multiple versions, indicated by tags.
The naming convention for Docker container images is: OWNER/CONTAINER_IMAGE_NAME:TAG
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Creating Your Own Container Images
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Dockerfile s specify what is within Docker container images.
The docker image build command is used to build a container image from a Dockerfile .
You can share your Docker container images through the Docker Hub so that others can create Docker containers from your container images.
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Creating More Complex Container Images
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Examples of Using Container Images in Practice
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Singularity: Getting started
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Singularity is another container platform and it is often used in cluster/HPC/research environments.
Singularity has a different security model to other container platforms, one of the key reasons that it is well suited to HPC and cluster environments.
Singularity has its own container image format (SIF).
The singularity command can be used to pull images from Sylabs Cloud Library and run a container from an image file.
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Using Singularity containers to run commands
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The singularity exec is an alternative to singularity run that allows you to start a container running a specific command.
The singularity shell command can be used to start a container and run an interactive shell within it.
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Using Docker images with Singularity
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The Singularity cache
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Singularity caches downloaded images so that an unchanged image isn’t downloaded again when it is requested using the singularity pull command.
You can free up space in the cache by removing all locally cached images or by specifying individual images to remove.
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Files in Singularity containers
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Your current directory and home directory are usually available by default in a container.
You have the same username and permissions in a container as on the host system.
You can specify additional host system directories to be available in the container.
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Using Singularity to run BLAST+
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We can use containers to run software without having to install it
The commands we use are very similar to those we would use natively
Singularity handles a lot of complexity around data and internet access for us
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Containers in Research Workflows: Reproducibility and Granularity
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Container images allow us to encapsulate the computation (and data) we have used in our research.
Using online containerimage repositories allows us to easily share computational work we have done.
Using container images along with a DOI service such as Zenodo allows us to capture our work and enables reproducibility.
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(Optional) Running MPI parallel jobs using Singularity containers
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Singularity images containing MPI applications can be built on one platform and then run on another (e.g. an HPC cluster) if the two platforms have compatible MPI implementations.
When running an MPI application within a Singularity container, use the MPI executable on the host system to launch a Singularity container for each process.
Think about parallel application performance requirements and how where you build/run your image may affect that.
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(Optional) Additional topics and next steps
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