The Living Thing / Notebooks :

Containerized apps

Doing things that previously took 1 computer using 0.75 computers

Usefulness: 🔧
Novelty: đź’ˇ
Uncertainty: 🤪 🤪 🤪
Incompleteness: 🚧 🚧 🚧

These are rapidly evolving standards. Check the timestamps on any advice.

A lighter, hipper alternative to virtual machines, which, AFAICT, attempts to make provisioning services more like installing an app than building a machine, because it aims to containerise apps rather than OSes, which emphasis leads to less dicking around, but somehow even more webinars.

Related to sandboxing, (and indeed they can even conflict because they use the same technologies) but different emphasis. Here the emphasis is more commonly upon you building some quick light-weight reproducible copy of a certain machine which you will send out into the world to do some thing, and it’s usually a server. Sandboxing is usually for apps, and usually on the desktop.

The most common hosts for containers are, or were, AFAICT, Linux-ish, but I believe there are also Windows/macOS solutions.

Docker

The most common way of doing this. It is fairly cimple structurally but is riven with confusing analogies and poor explanation.

Fortunately we have Julia Evans who explains the filesystem, overlayfs by example.

Docker gotchas

Secrets

Handling passwords is fiddly – see secrets.

Opaue timeout error

Do you get the following error?

Error response from daemon: Get https://registry-1.docker.io/v2/:
net/http: request canceled while waiting for connection
(Client.Timeout exceeded while awaiting headers)

According to thaJeztah, the solution is to use google DNS for Docker (or presumably some other non-awful DNS). You can set this by providing a JSON configuration in the preference panel (under daemon -> advanced), e.g.

{ "dns": [ "8.8.8.8", "8.8.4.4" ]}

Docker for reproducible research

Docker may not be the ultimate tool for reproducible research but it is a start. And it is convenient - see Keunwoo Choi’s guide for researchers by example. (🚧 fact-check the linked article.)

…How do you get your data in?

Tiffany Timbers gives a brisk run-through for academics.

Jon Zelner goes in-depth with R in a series culminating in continuous integration for science.

Reproducible research tuts has a docker (plus also VM-backed) tutorial.

Singularity

Singularity promises potentially useful container infrastructure.

Singularity provides a single universal on-ramp from the laptop, to HPC, to cloud.

USERS OF SINGULARITY CAN BUILD APPLICATIONS ON THEIR DESKTOPS AND RUN HUNDREDS OR THOUSANDS OF INSTANCES—WITHOUT CHANGE—ON ANY PUBLIC CLOUD.

Features include:

Released in 2016, Singularity is an open source-based container platform designed for scientific and high-performance computing (HPC) environments. Used by more than 25,000 top academic, government, and enterprise users, Singularity is installed on more than 3 million cores and trusted to run over a million jobs each day.

In addition to enabling greater control over the IT environment, Singularity also supports Bring Your Own Environment (BYOE)—where entire Singularity environments can be transported between computational resources (e.g., users’ PCs) with reproducibility.

GUIs

GUI comparison

LXC

LXC is another containerization standard. Because docker is a de facto default, let’s look at this in terms of docker