Introducing containers

Overview

Teaching: 30 min
Exercises: 10 min

Questions

• What are containers, and why might they be useful to me?

Objectives

• Show how software depending on other software leads to configuration management problems.

• Explain the notion of virtualisation in computing.

• Explain the ways in which virtualisation may be useful.

• Explain how containers streamline virtualisation.

Disclaimer

This looks like the Carpentries’ formatting of lessons because it is using their stylesheet (which is openly available for such purposes). However the similarity is visual-only: the lesson is not being developed by the Carpentries and has no association with the Carpentries.

The fundamental problem: software has dependencies that are difficult to manage

Consider Microsoft Excel: a typical workplace productivity tool. Most Excel users probably give little thought to the underlying software dependencies allowing them to open a given XLSX file on their computer. Indeed, in an ideal world none of us would need to think about fixing software dependencies, but we are far from that world. For example:

• Excel isn’t directly available for computers running Linux at all. So clearly Linux, as operating system software, is different from the Windows and macOS operating systems that do have Excel versions.
• Although XLSX is notionally standardised, Excel on macOS and Excel on Windows can interpret files differently. Clearly, despite looking similar, these two “Excel”s are clearly not precisely the same software.
  • Note that this macOS/Windows Excel situation is much better now than a few years ago: Microsoft had previously chosen to separately develop both of macOS Excel and Windows Excel, however when they also started releasing Office for iOS and Android, and providing web-based versions through Office 365, there was too much potential for divergence and compatibility chaos, so my understanding is that the core “engine” was standardised better across all the Office platforms. There still needs to be different software on each operating system that Excel supports to get that core “engine” up and running.
  • It is extremely unlikely that a current-day version of Excel would run on the Windows 2000 operating system. (A separate point is that it is also highly unlikely that it is a good idea to run Windows 2000 at all, given Microsoft has long stopped fixing its critical security flaws!) There are many other versions of Excel that either will or won’t run on all the other versions of Windows… and all of them may read and write XLS(X) files slightly differently, and potentially, incompatibly.

All of the above discussion is just about one piece of software: Microsoft Excel. Excel mostly just depends on the version of the operating system you’re running. However the situation gets far worse when building software in programming environments like R or Python. Those languages change over time, and depend on an enormous set of software libraries written by unrelated software development teams.

What if you wanted to distribute a software tool that automated interaction between R and Python. Both of these language environments have independent version and software dependency lineages. As the number of software components such as R and Python increases, this can rapidly lead to a combinatorial explosion in the number of possible configurations, only some of which will work as intended. This situation is sometimes informally termed “dependency hell”.

The situation is often mitigated in part by factors such as:

• an acceptance of inherent software and hardware obsolesce so it’s not expected that all versions of software need to be supported forever;
• some inherent synchronisation in the reasons for making software changes (e.g., the shift from 32-bit to 64-bit software), so not all versions will be expected to interact with all other versions.

It’s not very practical to have every version of every piece of software installed on any computer that might need to resolve dependencies, as the mostly-redundant space used by the different versions will continue to mount.

Thankfully there are ways to get underneath (a lot of) this mess: containers to the rescue! Containers provide a way to package up software dependencies and access to resources such as files and communications networks in a uniform manner.

Background: virtualisation in computing

Some uses of computers and the software they run should be deterministic, particularly when building reproducible computational environments. The meaning of “deterministic” is: if you feed in the same input, to the same computer, then the same output will appear.

However a computer running deterministic software, let’s call it the “guest”, should itself be able to be simulated as a deterministic computational process running on a computer we will call the “host”. The guest computer can be said to have been virtualised: it is no longer a physical computer. Note that “virtual machine” is frequently referred to using the abbreviation “VM”.

We have avoided the software dependency issue by looking for the lowest common factor across all software systems, which is the computer itself, beneath even the operating system software.

Omitting details and avoiding complexities…

Note that this description omits many details and avoids discussing complexities that are not particularly relevant to this introduction session, for example:

• Thinking with analogy to movies such as Inception, The Matrix, etc., can the guest computer figure out that it’s not actually a physical computer, and that it’s running as software inside a host physical computer? Yes, it probably can… but let’s not go there within this episode.
• Can you run a host as a guest itself within another host? Sometimes… but let’s not go there either.

Motivation for virtualisation

What features does virtualisation offer?

• Isolation: the VM is self-contained, so you can create and destroy it without affecting the host computer.
• Reproducibility: the VM can be “wound-back” to a known-good situation, much as you might revert a document you are editing to the last saved state.
• Manageability: the VM is software, so can be saved and restored as you might a document file (albeit a much larger file than a typical XLSX document!).
• Migration: the VM is just data, so can be transmitted to another physical host and run in the same way from there.
• Shareability: If you want to share your computational setup with someone else, you can trasmit the VM to another person and they can run it on their host - you do not need to send them your actual computer!

Downsides of “full” virtualisation:

• The file describing a VM has to contain its entire simulated hard-disk, so this leads to very large files.
• The guest computer wastes a lot of time managing “hardware” that’s not actually real, e.g., VMs need to boot up in the same way that your laptop does.
• A host needs lots of RAM to run large numbers of virtual machines, as the strong isolation means that the VMs do not share any resources.

Containers are a type of lightweight virtualisation

Containers are similar to virtual machines but offer a more lightweight solution. Containers sacrifice the strong isolation that full virtualisation provides in order to vastly reduce the resource requirements on the virtualisation host.

The term “container” can be usefully considered with reference to shipping containers. Before shipping containers were developed, packing and unpacking cargo ships was time consuming, and error prone, with high potential for different clients’ goods to become mixed up. Software containers standardise the packaging of a complete software system (the lightweight virtual machine): you can drop a container into a container host, and it should “just work”.

The same containers can run on:

• macOS;
• Microsoft Windows;
• Linux; and
• The Cloud

We should certainly see people using the same containers on macOS and Windows today.

And what do you do?

Talk to your neighbour, office mate or rubber duck about your research. How does computing help you do your research? How do you think containers (or virtualisation) could help you do more or better research?

Docker is a popular container platform

Docker is software that manages containers and the resources that containers need. While Docker is a leader in the container space, there are many similar technologies available… the concepts we learn today will allow us to use other container platforms even if their command syntax will be a little different.

Docker’s terminology

• Image: this is the term that Docker uses to describe the template for the virtual hard disk contents (files and folders) from which live instances of containers will be created. The term “container image” may sometimes be used to emphasise that the “image” relates to software containers and not, say, the sense of an “image” when discussing VMs or cute kitten pictures (without loss of generality).
  • If you are interested in more technical details, Docker actually creates images by combining together multiple Layers, although you can profitably use Docker without knowing much about layers. As a quick summary, each layer is a given set of files and folders. The combination of layers essentially involves a set-wise union of the files and folders in the layers, except that there is also a way for upper layers to hide files from lower layers (which has the appearance of deleting those files). Layers facilitate efficient storage space use, by allowing container images to share and reuse sets of files and folders, while still allowing individual container images to have their own specific files and folders.
• Container: this is an instance of a lightweight virtual machine created by Docker from a (container) image.
• Docker Hub: the Docker hub is a storage resource and associated website where a vast collection of preexisting container images are documented, and are made available for your use.

Key Points

• Almost all software depends on other software components to function, but these components have independent evolutionary paths.

• Projects involving many software components can rapidly run into a combinatoric explosion in the number of software version configurations available, yet only a subset of possible configurations actually works as desired.

• Containers collect software components together and can help avoid software dependency problems.

• Virtualisation is an old technology that container technology makes more practical.

• Docker is just one software platform that can create containers and the resources they use.