Building images with Docker

Overview

Teaching: 15 min
Exercises: 5 min

Questions

Objectives

• Discuss the pros&cons of building with Singularity vs Docker

• Learn the basic syntax of a Dockerfile

• Build and share an image with Docker

• Convert a Docker image into the Singularity format

Why using Docker for container builds?

Over the whole of this tutorial we’re proposing Singularity as the principal tool to handle and run containerised applications in HPC. Do we really need to extend our toolkit to include Docker?

To better inform an answer to this question, here are some of the advantages when building with one or the other tool.

Singularity

• Single file image, can be handled as any other file and shared easily;
• Unambiguous container usage modes, via distinct keywords: exec, shell, run, instance (see episode on web applications);
• Powerful ways of defining shell environment (see Singularity docs on Environment and Metadata);
• Ability to sign/verify images for improved security.

Docker

• Compatibility: image format can be run by all existing container engines, including Singularity;
• Layered image format allows caching, for reduced build time during prototyping and development.

Note how, at present, both tools require root privileges for building, implying that this step cannot be performed on HPC, and requires a dedicated machine instead.

Although Singularity builds offer some interesting advantages, there’s a single item that right now makes using Docker preferred in most situations.
It’s compatibility. Build with Docker, and you’ll know the resulting image can be run from every container engine anywhere in the world.

Container image formats

One of the differences between Docker and Singularity is the adopted format to store container images.

Docker adopts a layered format compliant with the Open Containers Initiative (OCI). Each build command in the recipe file results in the creation of a distinct image layer. These layers are cached during the build process, making them quite useful for development. In fact, repeated build attempts that make use of the same layers will exploit the cache, thus reducing the overall build time. On the other hand, shipping a container image is not straightforward, and requires either relying on a public registry, or compressing the image in a tar archive.

Since version 3.0, Singularity has developed the Singularity Image Format (SIF), a single file layout for container images, with extension .sif. Among the benefits, an image is simply a very large file, and thus can be transferred and shipped as any other file. Building on this single file format, a number of features have been developed, such as image signing and verification, and (more recently) image encryption. A drawback of this approach is that during build time a progressive, incremental approach is not possible.

Note that Singularity versions prior to 3.0 used different image formats, characterised by the extensions .simg or .sqsh. You can still find these around in the web; newer Singularity versions are still able to run them.

Building the container image with Docker

Let’s cd into the relevant demo directory:

$ cd $TUTO/demos/lolcow_docker

Let us also start building the image with docker build straight away. Meanwhile, we’ll bring the discussion on.

$ sudo docker build -t lolcow:1Nov19 .

In the command above, . is the location of the build context (i.e. the directory for the Dockerfile).
The -t flag is used to specify the image name (compulsory) and tag (optional).

Any lowercase alphanumeric string can be used as image name; here we’ve used lolcow. The image tag (following the colon) can be optionally used to maintain a set of different image versions on Docker Hub, and is a key feature in enabling reproducibility of your computations through containers; here we’ve used 1Nov19.

Adding the prefix <Your Docker Hub account>/ to the image name is also optional and allows to push the built image to your Docker Hub registry (see below).

The complete format for the image name looks like: <Your Docker Hub account ^>/<Image name>:<Image tag ^>. ^These are optional.

This is the output of our build:

Sending build context to Docker daemon  2.048kB
Step 1/7 : FROM ubuntu:18.04
 ---> 775349758637
Step 2/7 : LABEL maintainer="Pawsey Supercomputing Centre"
 ---> Running in 91c109dfd5ba
Removing intermediate container 91c109dfd5ba
 ---> 361490204a2c
Step 3/7 : RUN apt-get -y update &&   apt-get -y install fortune cowsay lolcat
 ---> Running in 4543b6bb99f1

[..]

Removing intermediate container 4543b6bb99f1
 ---> 7958a569068f
Step 4/7 : ENV PATH=/usr/games:$PATH
 ---> Running in 86282799c41f
Removing intermediate container 86282799c41f
 ---> 3ffdfe179e34
Step 5/7 : VOLUME /data
 ---> Running in f93de5446caa
Removing intermediate container f93de5446caa
 ---> 9c174e36bf3a
Step 6/7 : WORKDIR /data
 ---> Running in eed67d591239
Removing intermediate container eed67d591239
 ---> 36cc09b2c59b
Step 7/7 : CMD fortune | cowsay | lolcat
 ---> Running in 87a464d2ee67
Removing intermediate container 87a464d2ee67
 ---> 3c62a0f2e06e
Successfully built 3c62a0f2e06e
Successfully tagged lolcow:1Nov19

A Dockerfile recipe

The image we are building is very similar to the one we built with Singularity. Let’s have a look at its Dockerfile recipe file in the demo directory:

FROM ubuntu:18.04

LABEL maintainer="Pawsey Supercomputing Centre"

RUN apt-get -y update && \
  apt-get -y install fortune cowsay lolcat

ENV PATH=/usr/games:$PATH

VOLUME /data
WORKDIR /data

CMD fortune | cowsay | lolcat

The directory where the the Dockerfile is stored is the so called the Docker build context. Docker will include files in this directory in the build process and in the final image. As a by-product, this will make the build process longer and the image larger, so that we want to include only those strictly required for the build, even none if possible.

Let’s comment on the Docker instructions that appear in this Dockerfile.

• FROM: compulsory, it provides the starting image we will use to build our customised one;
• LABEL: used to add metadata information to the image, e.g. the maintainer, optional;
• RUN: this is the most used instruction, that allows to run most shell commands during the build. Multiple RUN instructions are often found in a single Dockerfile;
• ENV: set environment variables that will persist at runtime in the container; DO NOT use RUN export <..> to this end, as the variable will be lost after the RUN step is completed;
• VOLUME: creates a mount point ready to be used for mounting external (e.g. host) volumes; creates the corresponding directory if not existing;
• WORKDIR: changes directory to the specified path; the last current directory in the build will be the working directory in the running container.
  Note: if you use instead RUN cd <..>, the changed directory will only persist within that RUN instruction, and then be lost in subsequent build steps;
• CMD: specifies the default command to be executed with the container, in case no other command is provided.

More information on the Dockerfile syntax can be found at the Dockerfile reference.

Layers in a Docker image

Note how the RUN instruction above is used to execute a sequence of commands to update the list of available packages and install a set of Linux packages.
We have concatenated all these commands in one using the && linux operator, and then the \ symbol to break them into multiple lines for readability.

We could have used one RUN instruction per command, so why concatenating instead?
Well, each RUN creates a distinct layer in the final image, increasing its size. It is a good practice to use as few layers, and thus RUN instructions, as possible, to keep the image size smaller.

Syntax of recipe files: Singularity vs Docker

Task	Singularity	Docker
	Section	Directive
Starting image	Bootstrap + From	FROM
Linux commands	%post	RUN
Shell variables	%environment	ENV
Copying files	%files	COPY, ADD
Metadata	%labels, %help	LABEL
Default command	%runscript	CMD, ENTRYPOINT
Long running	%startscript	Not required
Work directory	Not required	WORKDIR
Mount points	Not required	VOLUME

List local Docker images

We know that Docker container images are not single files, but rather adopt a multi-layered format. To keep things tidy, Docker stores images and their layers in a hidden directory, under its own control.
To get the list of available images, including the ones you built, use docker images:

$ sudo docker images

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
lolcow              1Nov19              a67808f049be        5 hours ago         170MB

What if you need to debug the build process?

Quite often devising a recipe to install software involves a certain deal of trial and error.

If you need to inspect a Docker container during build, you can open an interactive shell session this way:

$ sudo docker run --rm -it ubuntu:18.04 bash

root@dd1ca993f4ad:/#

Here, -it keeps the container standard input open and allocates a terminal; --rm does some clean up when closing the session.

Note that Docker containers, unlike Singularity containers, are writable. So during an interactive sessions you can even trial software installations. However, edits are ephemeral, i.e. you lose them when you close the container.

When you’re done, type exit, or hit Ctrl-D, to leave the interactive shell.

Pushing the image to Docker Hub

If you have a (free) Docker Hub account you must first login to Docker.

$ sudo docker login

You are now ready to push your newly created image to the Docker Hub web registry.

First, let us create a second tag for the image, that includes your Docker Account. To this end we’ll use docker tag:

$ sudo docker tag lolcow:1Nov19 <your-dockerhub-account>/lolcow:1Nov19

Now we can push the image:

$ sudo docker push <your-dockerhub-account>/lolcow:1Nov19

The push refers to repository [docker.io/marcodelapierre/lolcow]
9d2959e72647: Pushed 
317d47a452af: Pushed 
e0b3afb09dc3: Mounted from library/ubuntu 
6c01b5a53aac: Mounted from library/ubuntu 
2c6ac8e5063e: Mounted from library/ubuntu 
cc967c529ced: Mounted from library/ubuntu 
1Nov19: digest: sha256:295c5695e2b05f6123bc2d8669ec7b66e45df5000ab9fc45ce3566ae3c0d839e size: 1571

Your image is now publicly available for anyone to pull.

Sharing the Docker image as a single file

If you don’t want to use an online registry to share your images, Docker allows you to convert them to a compressed tar.gz archive, which you can then share as any other large file, e.g. using scp, rsync, and other file transfer tools.
For instance, this can be useful when needing to transfer or share images including proprietary software, amongst collaborators that own the appropriate license.

Use docker save to create the archive:

$ sudo docker save -o lolcow_1Nov19.tar.gz lolcow:1Nov19

After the transfer, use docker load to extract the image in a format that is usable by Docker:

$ sudo docker load -i lolcow_1Nov19.tar.gz

Loaded image: lolcow:1Nov19

Note: you need Docker to extract the image from the compressed archive, Singularity can’t do it.

Running the image with Docker

Let’s give this image a go! Let’s execute it without any argument to use the default command:

$ sudo docker run --rm lolcow:1Nov19

 _______________________________________
/ Good news. Ten weeks from Friday will \
\ be a pretty good day.                 /
 ---------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Note how the default command can be readily overwritten:

$ sudo docker run --rm lolcow:1Nov19 echo "Hello World!"

Hello World!

Converting and running the image with Singularity

We’ve created a container image using Docker. Now, what steps are required to use it with Singularity?
As seen in a previous episode, the Singularity pull command can take care of converting a Docker image for its own usage.

If you have pushed the image to Docker Hub, just execute:

$ singularity pull docker://<your-dockerhub-account>/lolcow:1Nov19

If your Docker-equipped machine also comes with Singularity, you can also grab the image from the local image repo, using the docker-daemon: prefix. Due to a current bug in Singularity, you will need to ditch the double slashes //:

$ singularity pull docker-daemon:lolcow:1Nov19

Does it work?

$ ./lolcow_1Nov19.sif

 ________________________________________
/ Don't go surfing in South Dakota for a \
\ while.                                 /
 ----------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Sure it does!

Bonus: example Dockerfiles

Have a look at these, just to get a taste of what a production Dockerfile might look like.

Pawsey MPI-base image

Dockerfile

FROM ubuntu:18.04

LABEL maintainer="brian.skjerven@pawsey.org.au"

# Install package dependencies
RUN apt-get update -qq \
      && apt-get -y --no-install-recommends install \
         build-essential \
         gdb \
         gfortran \
         wget \
      && apt-get clean all \
      && rm -r /var/lib/apt/lists/*


### Build MPICH ###

ARG MPICH_VERSION="3.1.4"
ARG MPICH_CONFIGURE_OPTIONS="--enable-fast=all,O3 --prefix=/usr"
ARG MPICH_MAKE_OPTIONS="-j4"

WORKDIR /tmp/mpich-build

RUN wget http://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz \
      && tar xvzf mpich-${MPICH_VERSION}.tar.gz \
      && cd mpich-${MPICH_VERSION}  \
      && ./configure ${MPICH_CONFIGURE_OPTIONS} \
      && make ${MPICH_MAKE_OPTIONS} \
      && make install \
      && ldconfig


### Build OSU Benchmarks ###

ARG OSU_BENCH_VERSION="5.4.2"
ARG OSU_BENCH_CONFIGURE_OPTIONS="--prefix=/usr/local CC=mpicc CXX=mpicxx CFLAGS=-O3"
ARG OSU_BENCH_MAKE_OPTIONS="-j4"

WORKDIR /tmp/osu-benchmark-build

RUN wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-${OSU_BENCH_VERSION}.tar.gz \
      && tar xzvf osu-micro-benchmarks-${OSU_BENCH_VERSION}.tar.gz \
      && cd osu-micro-benchmarks-${OSU_BENCH_VERSION} \
      && ./configure ${OSU_BENCH_CONFIGURE_OPTIONS} \
      && make ${OSU_BENCH_MAKE_OPTIONS} \
      && make install

WORKDIR /
RUN rm -rf /tmp/*
CMD ["/bin/bash"]

A simple Python image

Dockerfile

FROM continuumio/miniconda3:4.5.11

LABEL maintainer="marco.delapierre@pawsey.org.au"

RUN apt-get clean all && \
    apt-get update && \
    apt-get upgrade -y && \
    apt-get install -y \
        vim && \
    conda update -y conda \
    && apt-get clean all && \
    apt-get purge && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ARG atlas_version="2.0.1"
RUN conda install -y -c bioconda -c conda-forge metagenome-atlas="$atlas_version"

RUN mkdir /databases && \
    chmod go+w /databases

RUN mkdir /home/none && \
    mkdir /home/none/.cache && \
    cp -p $HOME/.bashrc $HOME/.profile /home/none/ && \
    chmod -R go+w /home/none
ENV HOME="/home/none"
VOLUME /data
WORKDIR /data

A large R image

Dockerfile

FROM rocker/tidyverse:latest

RUN apt-get update -qq && apt-get -y --no-install-recommends install \
      autoconf \
      automake \
      g++ \
      gcc \
      gfortran \
      make \
      && apt-get clean all \
      && rm -rf /var/lib/apt/lists/*

RUN mkdir -p $HOME/.R
COPY Makevars /root/.R/Makevars

RUN Rscript -e "library('devtools')" \
      -e "install_github('Rdatatable/data.table', build_vignettes=FALSE)" \
      -e "install.packages('reshape2')" \
      -e "install.packages('fields')" \
      -e "install.packages('ggbeeswarm')" \
      -e "install.packages('gridExtra')" \
      -e "install.packages('dynamicTreeCut')" \
      -e "install.packages('DEoptimR')" \
      -e "install.packages('http://cran.r-project.org/src/contrib/Archive/robustbase/robustbase_0.90-2.tar.gz', repos=NULL, type='source')" \
      -e "install.packages('dendextend')" \
      -e "install.packages('RColorBrewer')" \
      -e "install.packages('locfit')" \
      -e "install.packages('KernSmooth')" \
      -e "install.packages('BiocManager')" \
      -e "source('http://bioconductor.org/biocLite.R')" \
      -e "biocLite('Biobase')" \
      -e "biocLite('BioGenerics')" \
      -e "biocLite('BiocParallel')" \
      -e "biocLite('SingleCellExperiment')" \
      -e "biocLite('GenomeInfoDb')" \
      -e "biocLite('GenomeInfgoDbData')" \
      -e "biocLite('DESeq')" \
      -e "biocLite('DESeq2')" \
      -e "BiocManager::install(c('scater', 'scran'))" \
      -e "library('devtools')" \
      -e "install_github('IMB-Computational-Genomics-Lab/ascend', ref = 'devel')" \
      && rm -rf /tmp/downloaded_packages

Key Points

• Use FROM to specify the build starting image

• Execute shell commands with RUN

• Declare environment variables with ENV

• Build images starting from a Dockerfile recipe with docker build

• Push images to a web registry with docker push

• Share images as a single file using docker save and docker load

• You can locally convert a Docker image by using singularity pull docker-daemon: