Peter Solymos for Analythium

Posted on May 31, 2021 • Updated on Aug 25, 2021 • Originally published at hosting.analythium.io

Best Practices for R with Docker

#docker #rstats #shiny

The use of Docker with R has been transformative in many
ways
over the past 5 years. What is common in this diversity of use cases is
that the Docker images almost always start with a parent image. What
parent image you use? How do you add new layers to it? These questions
will determine how quickly you can iterate while in development, and the
size of the final image you send to production. In this post, I will
compare using different parent images and outline best practices. I
focus on Shiny apps but most of these ideas apply generally to any
dockerized R application, like images for compute jobs or interfaces.

Parent images

In the previous post, we explored dependency management for Shiny
apps
using the rocker/r-ubuntu:20.04 as the parent image. A parent image is
an image that you define in the FROM directive of the Dockerfile. A
base image
has FROM scratch as the first line. The R base images start with
parent images. For example, the R Ubuntu image starts with
FROM ubuntu:focal.

Here are the four commonly used parent images for R:

docker pull rhub/r-minimal:4.0.5
docker pull rocker/r-base:4.0.4
docker pull rocker/r-ubuntu:20.04
docker pull rstudio/r-base:4.0.4-focal

The image sizes vary quite a bit with the Alpine Linux base
rhub/r-minimal being smallest and the Ubuntu-based rstudio/r-base
25x the size of the smallest image:

$ docker images

REPOSITORY          TAG                 SIZE
rhub/r-minimal      4.0.5               35.3MB
rocker/r-base       4.0.4               761MB
rocker/r-ubuntu     20.04               673MB
rstudio/r-base      4.0.4-focal         894MB

The Debian Linux based rocker/r-base Docker image from the
Rocker
project is considered bleeding edge when it comes to system
dependencies, i.e. latest development versions are usually available
sooner than on other Linux distributions.

The two Ubuntu Linux based images, rocker/r-ubuntu and
rstudio/r-base from the
Rocker
project and from RStudio are for
long-term support Ubuntu versions and use the
RSPM CRAN binaries.

The Alpine Linux based rhub/r-minimal Docker image from the
r-hub project is preferred for its
small image sizes.

Using BildKit

Docker versions 18.09 or higher come with a new opt-in builder backend
called BuildKit. BuildKit prints out
a nice summary of each layer including timing for the layers and the
overall build. This is the general build command that I used to compare
the four parent images:

DOCKER_BUILDKIT=1 docker build --no-cache -f $FILE -t $IMAGE .

BuildKit backend is enabled by turning on the DOCKER_BUILDKIT=1
environment variable. I use the --no-cache option to avoid using
cached layers, thus having a fair assessment of build times (you usually
only build 1 and not 4). The -f $FILE flag allows building from
different files kept in the same folder.

All the code used here can be found in this GitHub repository, look in
the folder 99-images:

Image build times

This is the script I used to build the four images with BuildKit:

# rhub/r-minimal
export IMAGE="analythium/covidapp-shiny:minimal"
export FILE="Dockerfile.minimal"
DOCKER_BUILDKIT=1 docker build --no-cache -f $FILE -t $IMAGE .

# rocker/r-base
export IMAGE="analythium/covidapp-shiny:base"
export FILE="Dockerfile.base"
DOCKER_BUILDKIT=1 docker build --no-cache -f $FILE -t $IMAGE .

# rocker/r-ubuntu
export IMAGE="analythium/covidapp-shiny:ubuntu"
export FILE="Dockerfile.ubuntu"
DOCKER_BUILDKIT=1 docker build --no-cache -f $FILE -t $IMAGE .

# rstudio/r-base
export IMAGE="analythium/covidapp-shiny:focal"
export FILE="Dockerfile.focal"
DOCKER_BUILDKIT=1 docker build --no-cache -f $FILE -t $IMAGE .

I changed the CRAN repository for the Debian and Ubuntu Rocker images to
see timing differences between installing packages as binary or from
source. Total build times (on a 6-year old MacBook Pro) were the
following:

rhub/r-minimal: 27 minutes with building packages from source
rocker/r-base: 12 minutes when building from source, 2.9 minutes when installing binary packages
rocker/r-ubuntu: 12 minutes when building from source, 3.2 minutes when installing binary packages
rstudio/r-base: 3.1 minutes with installing binary packages

The difference between the binary vs. source package installs is
expected. What is interesting is the 12 vs. 27 minutes between the
Debian/Ubuntu images and the minimal Alpine image. Is it worth waiting
for?

Image sizes

I got the image sizes from docker images and made a small data frame
in R to calculate the size difference between the final and parent
images:

x = data.frame(TAG=c("minimal", "base", "ubuntu", "focal"),
  PARENT_SIZE=c(35, 761, 673, 894) / 1000, # base image
  FINAL_SIZE=c(222 / 1000, 1.05, 1.22, 1.38)) # final image

x$DIFF = x$FINAL_SIZE - x$PARENT_SIZE

#       TAG PARENT_SIZE FINAL_SIZE  DIFF
# 1 minimal       0.035      0.222 0.187
# 2    base       0.761      1.050 0.289
# 3  ubuntu       0.673      1.220 0.547
# 4   focal       0.894      1.380 0.486

The image sizes themselves differed quite a bit, the RStudio Ubuntu
image was 6.2x larger than the minimal R image. Size differences were
similarly different.

Image sizes can be deceiving. It might not matter much if images are
large if for example, we have multiple images sharing some of the
layers
(i.e. ones from the parent image). The CPU and RAM footprint of the
containers might also be unrelated to the image sizes. But it might
impact "cold start" performance when images are pulled to an empty
server.

Alpine Linux based image

The Dockerfiles and the build experience for the Ubuntu and Debian
images were very similar. Build times and image sizes were also
comparable. The Alpine Linux-based minimal image took the longest time
to build but resulted in the smallest image size. The Dockerfile for
this setup also looks quite different from the Debian/Ubuntu setup:

FROM rhub/r-minimal:4.0.5

RUN apk update
RUN apk add --no-cache --update-cache \
    --repository http://nl.alpinelinux.org/alpine/v3.11/main \
    autoconf=2.69-r2 \
    automake=1.16.1-r0 \
    bash tzdata
RUN echo "America/Edmonton" > /etc/timezone

RUN installr -d \
    -t "R-dev file linux-headers libxml2-dev gnutls-dev openssl-dev libx11-dev cairo-dev libxt-dev" \
    -a "libxml2 cairo libx11 font-xfree86-type1" \
    remotes shiny forecast jsonlite ggplot2 htmltools plotly Cairo

RUN rm -rf /var/cache/apk/*

RUN addgroup --system app && adduser --system --ingroup app app
WORKDIR /home/app
COPY app .
RUN chown app:app -R /home/app
USER app

EXPOSE 3838

CMD ["R", "-e", "options(tz='America/Edmonton');shiny::runApp('/home/app', port = 3838, host = '0.0.0.0')"]

The base image is so bare-bones that it needs to install time zones,
fonts and the Cairo device for ggplot2 to work (read the limitations
here). Instead of
apt you have apk and might have to work a bit harder to find all the
Alpine-specific dependencies.

One interesting aspect of this image is that instead of the littler
utilities familiar from the Rocker images, we have the very similar
installr script that installs R packages and system requirements:

the -d flag installs then removes compilers ( gcc, musl-dev, g++), as these are typically not needed on the final image;
system packages listed after the -t flag are removed after the R packages have been installed;
system packages listed after the -a flag are run-time dependencies that are needed for the packages to function properly and are not removed from the image.

The installation of the system packages – that are all available on the
other parent images – contributes to the longer build times. The
BuildKit output gives you a clue about where exactly the time was spent.

The rest of the Dockerfile is very similar to the other distributions:
add Linux user, copy files, expose port, define the entrypoint command.
But how do you figure out what system packages you need?

System packages

First of all, each package lists its system requirements. These are
usually run-time dependencies that the package needs to properly
function. So check that first.

There are at least two databases listing package requirements: one
maintained by
RStudio (this
supports RSPM), another one by
R-hub. Both of these list system
packages for various Linux distributions, macOS, and Windows. But even
with these databases, the build- vs. run-time dependencies can be
sometimes hard to distinguish. Build-time system libraries are always
named with a -dev or -devel postfix. Read the vignette of the
maketools
R package by Jeroen Ooms for a nice explanation and a suggested workflow
for determining run-time dependencies of packages.

Best practices

Based on these results and the list of Dockerfile best
practices,
here are a few suggestions to improve the developer experience and the
quality of the final Docker images.

1. Minimize dependencies

Avoid installing "nice to have" packages and do not start from
general-purpose parent images aimed at interactive use. Images for Shiny
apps and other web services benefit from keeping the images as lean as
possible by adding those R packages and system requirements that are
absolutely necessary. Multi-stage
builds
can be helpful to only include artifacts that are needed.

2. Use caching

When building an image, Docker executes each instruction in the order
specified in the Dockerfile. Docker looks for an existing image in its
cache that it can reuse, rather than creating a new (duplicate) image.
Only the instructions RUN, COPY, ADD create layers:

for the RUN instructions, just the command string from the Dockerfile is used to find a match from an existing image;
for the ADD and COPY instructions, the contents of the file(s) in the image are examined and a checksum is calculated for each file;
the last-modified and last-accessed times of the file(s) are not considered in these checksums for the ADD and COPY instructions.

3. Order layers

Caching can be useful is when installing R package dependencies. In a
previous post, we looked at how to use the renv
package
to install dependencies. Here is a simplified snippet from
that
Dockerfile:

## install dependencies
COPY ./renv.lock .
RUN Rscript -e "renv::restore()"

## copy the app
COPY app .

What would happen if we switched the two blocks?

## copy the app
COPY app .

## install dependencies
COPY ./renv.lock .
RUN Rscript -e "renv::restore()"

You would have to wait for the build to reinstall all the R packages
whenever the app files have changed. This is because once the cache is
invalidated all subsequent Dockerfile commands generate new images
instead of using the cache.

It is best to order the instructions in your Dockerfile from the less
frequently changed to the more frequently changed. This ensures that the
build cache is reusable.

Order Dockerfile instructions from the less to the more frequently changed

4. Switch user

Running the container with root privileges allows unrestricted use which
is to be avoided in production. Although you can find lots of examples
on the Internet where the container is run as root, this is generally
considered bad practice. Use something like this:

RUN addgroup --system app \

    && adduser --system --ingroup app app

WORKDIR /home/app

COPY app .

RUN chown app:app -R /home/app

USER app

Use linter

Best practices for writing Dockerfiles are being followed more and more
often according to this paper
after mining more than 10 million Dockerfiles on Docker Hub and GitHub.
However, there is still room for improvement. This is where
linters come in as
useful tools for static code analysis.
Hadolint lists lots of
rules for Dockerfiles and is available as a VS Code
extension.

Summary

This post started with a simple premise: compare the four most commonly
used parent images for R and draw some conclusions. It became a really
long post, but I believe it gives a good rationale for following a few
basic suggestions that can hugely improve the developer experience and
the quality of the final Docker images.

Top comments (4)

Pinei • Sep 4 '21 • Edited

Great post. I am trying to build an image for a recent version of rstudio server using "fdewes/rstudio-server-arm64" as reference (yes, it is for raspberry pi).

Just got an error with NPM or YARN. After get it working I will need those tips in this article to make some cleaning and the "multi stage build" path.

Peter Solymos • Sep 10 '21

Thanks! Not sure why you are getting NPM/YARN errors from that image build though.

Pinei • Sep 27 '21

Just got a working image ... need a time to implement the best practices, including "multi stage build"

github.com/pinei/edgyR-pi

Peter Solymos • Oct 2 '21

Wow. You really made some progress there! That's really good to see. I am thinking of entering the Raspberry edge world myself, this'll be a good starting point for sure.

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