An introduction to Docker and its role in sustainable research

Andre Weiner, Mathematical Modeling and Analysis (Chair of Prof. D. Bothe), TU Darmstadt
Get in touch: weiner@mma.tu-darmstadt.de
Slides available at: andreweiner.github.io/reveal.js/mma_docker_intro.html

Some warm-up questions

answer by a show of hands

What is Docker?

Who is using Docker images?

Who has created Docker images?

What is Git and Github/Bitbucket?

Who is working with Git and Github/Bitbucket?

Binary code?

Shared object libraries (.so)?

Outline

Introduction to Docker
Using a Docker image
Containerizing an applicaton
Containerizing OpenFOAM
Containerizing a single application more effectively
Containerizing a Jupyter notebook
Distributing images

It's a training ...

Feel free to ask questions at any time!

Introduction to Docker®

Just enough to get you started

What is Docker?

Docker is a tool to create an isolated environment inside your OS. The environment is called container.

What is Docker?

Docker is a tool for OS-level virtualization. OS-level virtualization allows the existence of multiple isolated user-space instances, so-called containers.

VM versus Docker

Image source

Why call it container?

What is a container?

“A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another.”

Source

What is a container image?

“A Docker container image is a lightweight, standalone, executable package of software that includes everything needed to run an application: code, runtime, system tools, system libraries and settings.”

Source

Image versus Container

Image source CD, Image source PC

Containers in research

Docker minimizes local dependencies!

reproducible results (long term)
easy sharing of software
quick and risk free testing
automated testing and deployment
Cloud computing

Compatibility

Linux kernel 3.10+ (30th June 2013)
Docker engine
- Initial release: 0.1.0 (23rd March 2013)
- Compatibility break: 1.10 (4th Febuary 2016)
- Current release: 19.03.01 (25th July 2019)

Docker group

The docker engine requires root previliges, so you can

run every command with sudo, or
create a docker group

sudo groupadd docker

sudo usermod -aG docker $USER

Using a Docker image

Download the installOpenFOAM and startOpenFOAM scripts (ESI version)


~$ chmod +x installOpenFOAM
~$ ./installOpenFOAM
~$ chmod +x startOpenFOAM
~$ ./startOpenFOAM
# in the container command line prompt
~$ mkdir -p $FOAM_RUN
~$ run
~$ cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity/cavity .
~$ cd cavity
~$ blockMesh
~$ icoFoam

Observations

Command line promt?
bash-4.2$
HOST?
echo $HOSTNAME
Username?
whoami
Directory?
pwd
Where is the data?

installOpenFOAM


username="$USER"
user="$(id -u)"
home="${1:-$HOME}"

imageName="openfoamplus/of_v1906_centos73"
containerName="of_v1906"

docker run  -it -d --name ${containerName} --user=${user}  \
  -e USER=${username}                                      \
  --workdir="${home}"                                      \
  --volume="${home}:${home}"                               \
  --volume="/etc/group:/etc/group:ro"                      \
  --volume="/etc/passwd:/etc/passwd:ro"                    \
  --volume="/etc/shadow:/etc/shadow:ro"                    \
  --volume="/etc/sudoers.d:/etc/sudoers.d:ro"              \
  -v=/tmp/.X11-unix:/tmp/.X11-unix ${imageName}            \
  /bin/bash --rcfile /opt/OpenFOAM/setImage_v1906.sh

docker run (container creation)


docker run [options] IMAGE_NAME [command] [arguments]

Show images


docker image ls
...
REPOSITORY                       TAG                 IMAGE ID            CREATED             SIZE
openfoamplus/of_v1906_centos73   latest              6e63df7efb1e        5 weeks ago         2.23GB

Show running containers


docker container ls
...
CONTAINER ID  IMAGE                           COMMAND                 CREATED      STATUS      PORTS  NAMES
9176100c3273  openfoamplus/of_v1906_centos73  "/bin/bash --rcfile …"  5 weeks ago  Up 5 weeks         of_v1906

Show all containers


docker container stop 9176100c3273
docker container ls -a
...
CONTAINER ID  IMAGE                           COMMAND                 CREATED      STATUS                      PORTS  NAMES
9176100c3273  openfoamplus/of_v1906_centos73  "/bin/bash --rcfile …"  5 weeks ago  Exited (137) 6 seconds ago         of_v1906

Removing images and containers

Remove images
docker image rm IMAGE_IDs
Remove all unsed images
docker image prune
Remove containers
docker container rm CONTAINER_IDs
Remove all stopped containers
docker container prune

startOpenFOAM


xhost +local:of_v1906
docker start of_v1906
docker exec -it of_v1906 /bin/bash -rcfile /opt/OpenFOAM/setImage_v1906.sh

docker start (start a stopped container)


docker start CONTAINER_NAME # or CONTAINER_ID

docker exec (run a command in a running container)


docker exec [options] CONTAINER_NAME COMMAND [arguments]

Learn more

Containerizing an application

Scenario

You develop a new app based on a specific framework (e. g. OpenFOAM, Jupyter, ...)
You do not modify the framework itself
There is already a Docker image for the version of the framework you are working with
You want to share/save framework and app together (complete build environment)

Repo: of_app_isolation


git clone https://github.com/AndreWeiner/of_app_isolation.git
cd of_app_isolation
ls
...
Dockerfile
Dockerfile.single
README.md


git clone https://github.com/AndreWeiner/dummyFoam
git --git-dir dummyFoam/.git log -1
...
commit f2fbf951ca312e98b3e9c13def8ec122089d67e4
Author: Andre Weiner <weiner@mma.tu-darmstadt.de>
Date:   Fri Jun 28 12:57:23 2019 +0200

    Update to OpenFOAM-v1906.


git --git-dir dummyFoam/.git log -1 --format=%h
...
f2fbf95

Dockerfile.single


FROM openfoamplus/of_v1906_centos73
# copy app source code to base image
COPY dummyFoam /opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam
# change working directory
WORKDIR /opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam
# source environment variables, compile, and create execution script
RUN source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
    wmake && \
    mkdir /case && \
    echo "source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc &> \
    /dev/null; dummyFoam -case /case" > /runDummyFoam.sh

Best pratices for writing Dockerfiles

Building the image


# -t TAG
# -f DOCKERFILE
#  . current path
docker build -t andreweiner/dummy_foam:$(git --git-dir dummyFoam/.git log -1 --format=%h) -f Dockerfile.single .
...
docker image ls
REPOSITORY              TAG      IMAGE ID      CREATED         SIZE
andreweiner/dummy_foam  f2fbf95  50a4ab4d3441  13 seconds ago  2.23GB

docker build


docker build [options] PATH
# tag syntax
-t repository/app_name:version
# multiple tags are possible
-t repo/my_app:v1.0 -t repo/my_app:latest

Using the app


# go to some valid OpenFOAM case
cd ${HOME}/OpenFOAM/${USER}-v1906/run/cavity
docker container run -it -v"$PWD:/case" andreweiner/dummy_foam:f2fbf95 /bin/bash /runDummyFoam.sh
...
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time


ExecutionTime = 0 s  ClockTime = 0 s

End

Containerizing OpenFOAM

Scenario

You wrote an app or a library from scratch
You modified an app or a library substantially
You want to share/save framework and app together (complete build environment)

steps to go

build a build system like the one you work with
add the sources and build them

repository: of_pytorch_docker


git clone https://github.com/AndreWeiner/of_pytorch_docker.git

Download the OpenFOAM-v1906 sources: link

Dockerfile


FROM ubuntu:18.04
# install dependencies to compile OpenFOAM
RUN apt-get update && apt-get install -y build-essential flex bison cmake zlib1g-dev \
  libboost-system-dev libboost-thread-dev libopenmpi-dev openmpi-bin gnuplot \
  libreadline-dev libncurses-dev libxt-dev wget unzip vim
# copy OpenFOAM sources to the image
COPY OpenFOAM-v1906.tgz /opt/
# extract sources and prepare compilation
RUN mkdir /opt/OpenFOAM && \
  tar -xzf /opt/OpenFOAM-v1906.tgz -C /opt/OpenFOAM && \
  rm /opt/*.tgz
# set default shell to bash to source OpenFOAM specific environment variables
SHELL ["/bin/bash", "-c"]
# change installation directory to /opt/OpenFOAM and add default compilation flag -D_GLIBCXX_USE_CXX11_ABI=0
WORKDIR /opt/OpenFOAM/OpenFOAM-v1906
RUN sed -i '/projectDir=\"\$HOME\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"/c\projectDir=\"\/opt\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"' /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
  sed -i '/CC          = g++ -std=c++11/c\CC          = g++ -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=0' /opt/OpenFOAM/OpenFOAM-v1906/wmake/rules/General/Gcc/c++ && \
  source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && ./Allwmake -j 8
# get libtorch and set enironment variable with installation folder
WORKDIR /opt
RUN wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-latest.zip && \
    unzip libtorch-shared-with-deps-latest.zip && \
    rm libtorch*.zip
ENV TORCH_LIBRARIES /opt/libtorch


FROM ubuntu:18.04
# install dependencies to compile OpenFOAM
RUN apt-get update && apt-get install -y build-essential flex bison cmake zlib1g-dev \
  libboost-system-dev libboost-thread-dev libopenmpi-dev openmpi-bin gnuplot \
  libreadline-dev libncurses-dev libxt-dev wget unzip vim
# copy OpenFOAM sources to the image
COPY OpenFOAM-v1906.tgz /opt/
# extract sources and prepare compilation
RUN mkdir /opt/OpenFOAM && \
  tar -xzf /opt/OpenFOAM-v1906.tgz -C /opt/OpenFOAM && \
  rm /opt/*.tgz
# set default shell to bash to source OpenFOAM specific environment variables
SHELL ["/bin/bash", "-c"]
# change installation directory to /opt/OpenFOAM and add default compilation flag -D_GLIBCXX_USE_CXX11_ABI=0
WORKDIR /opt/OpenFOAM/OpenFOAM-v1906
RUN sed -i '/projectDir=\"\$HOME\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"/c\projectDir=\"\/opt\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"' /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
  sed -i '/CC          = g++ -std=c++11/c\CC          = g++ -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=0' /opt/OpenFOAM/OpenFOAM-v1906/wmake/rules/General/Gcc/c++ && \
  source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && ./Allwmake -j 8
# get libtorch and set enironment variable with installation folder
WORKDIR /opt
RUN wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-latest.zip && \
    unzip libtorch-shared-with-deps-latest.zip && \
    rm libtorch*.zip
ENV TORCH_LIBRARIES /opt/libtorch


FROM ubuntu:18.04
# install dependencies to compile OpenFOAM
RUN apt-get update && apt-get install -y build-essential flex bison cmake zlib1g-dev \
  libboost-system-dev libboost-thread-dev libopenmpi-dev openmpi-bin gnuplot \
  libreadline-dev libncurses-dev libxt-dev wget unzip vim
# copy OpenFOAM sources to the image
COPY OpenFOAM-v1906.tgz /opt/
# extract sources and prepare compilation
RUN mkdir /opt/OpenFOAM && \
  tar -xzf /opt/OpenFOAM-v1906.tgz -C /opt/OpenFOAM && \
  rm /opt/*.tgz
# set default shell to bash to source OpenFOAM specific environment variables
SHELL ["/bin/bash", "-c"]
# change installation directory to /opt/OpenFOAM and add default compilation flag -D_GLIBCXX_USE_CXX11_ABI=0
WORKDIR /opt/OpenFOAM/OpenFOAM-v1906
RUN sed -i '/projectDir=\"\$HOME\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"/c\projectDir=\"\/opt\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"' /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
  sed -i '/CC          = g++ -std=c++11/c\CC          = g++ -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=0' /opt/OpenFOAM/OpenFOAM-v1906/wmake/rules/General/Gcc/c++ && \
  source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && ./Allwmake -j 8
# get libtorch and set enironment variable with installation folder
WORKDIR /opt
RUN wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-latest.zip && \
    unzip libtorch-shared-with-deps-latest.zip && \
    rm libtorch*.zip
ENV TORCH_LIBRARIES /opt/libtorch

Building the image

Don't build it now! It takes ~50min...


# docker build -t your_dockerhub/of_pytorch:your_tag .
# be expressive ...
docker build -t andreweiner/of_pytorch:of1906-py1.1-cpu

Containerizing a single application more effectively

dummyFoam dependencies


docker container run -it andreweiner/dummy_foam:f2fbf95 /bin/bash
...
source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc
ldd $(which dummyFoam)
...
libfiniteVolume.so => /opt/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so (0x00007fbce0318000)
libmeshTools.so => /opt/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libmeshTools.so (0x00007fbcdfada000)
libOpenFOAM.so => /opt/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so (0x00007fbcdef0d000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fbcded09000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fbcdea00000)
libm.so.6 => /lib64/libm.so.6 (0x00007fbcde6fe000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fbcde4e8000)
libc.so.6 => /lib64/libc.so.6 (0x00007fbcde125000)
...
exit

Multistage builds

Repository: of_app_isolation

Build the app as done before
Create a new, clean image
Copy only executable and dependencies

The final image will be significantly smaller!

Dockerfile: stage I


FROM openfoamplus/of_v1906_centos73 AS builder
COPY dummyFoam /opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam
WORKDIR /opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam
RUN source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
    wmake && \
    ldd $(which dummyFoam) | cut -d" " -f3 | xargs tar --dereference -cf libs.tar && \
    tar --dereference -rvf libs.tar /lib64/ld-linux-x86-64.so.2 && \
    tar -cf etc.tar /opt/OpenFOAM/OpenFOAM-v1906/etc

Dockerfile: stage II


FROM alpine:latest
RUN apk add --no-cache bash tar
COPY --from=builder /opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam/libs.tar \
										/root/OpenFOAM/-v1906/platforms/linux64GccDPInt32Opt/bin/dummyFoam \
										/opt/OpenFOAM/OpenFOAM-v1906/applications/solvers/dummyFoam/etc.tar \
										/
RUN tar -xf libs.tar && \
		tar -xf etc.tar && \
		rm *.tar && \
		sed -i '/projectDir=\"\$HOME\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"/c\projectDir=\"\/opt\/OpenFOAM\/OpenFOAM-\$WM_PROJECT_VERSION\"' /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc && \
		mkdir case && \
		echo "source /opt/OpenFOAM/OpenFOAM-v1906/etc/bashrc &> /dev/null; /dummyFoam -case /case" > runDummyFoam.sh
ENV LD_LIBRARY_PATH=/opt/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib:\
lib:lib64:/opt/OpenFOAM/ThirdParty-v1906/platforms/linux64Gcc/openmpi-1.10.4/lib64/lib:\
/opt/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/openmpi-1.10.4:\
/opt/OpenFOAM/ThirdParty-v1906/platforms/linux64Gcc/openmpi-1.10.4/lib64

Building the image


# -t TAG
# -f DOCKERFILE
#  . current path
docker build -t andreweiner/dummy_foam_iso:$(git --git-dir dummyFoam/.git log -1 --format=%h) .
...
docker image ls
REPOSITORY                  TAG      IMAGE ID      CREATED         SIZE
andreweiner/dummy_foam_iso  f2fbf95  018fbad986dd  5 weeks ago     161MB

The previous image was ~2.3GB

Using the app


# go to some valid OpenFOAM case
cd ${HOME}/OpenFOAM/${USER}-v1906/run/cavity
docker container run -it -v"$PWD:/case" andreweiner/dummy_foam_iso:f2fbf95 /bin/bash /runDummyFoam.sh
...
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time


ExecutionTime = 0 s  ClockTime = 0 s

End

Containerizing Jupyter notebooks

Distributing an image

Sharing images

public registry (Dockerhub)
private registry
tar ball

Dockerhub

To use Dockerhub, you need an account (free).


docker login --username=yourhubusername --email=name@host.com
docker push andreweiner/of_pytorch:of1906-py1.1-cpu
...
docker pull andreweiner/of_pytorch:of1906-py1.1-cpu

Check out the of_pytorch example!

tar archive


docker history andreweiner/dummy_foam:f2fbf95
...
IMAGE         CREATED       CREATED BY                                     SIZE    COMMENT
50a4ab4d3441  17 hours ago  /bin/sh -c source /opt/OpenFOAM/OpenFOAM-v19…  72.5kB
1d1a83fdb3da  17 hours ago  /bin/sh -c #(nop) WORKDIR /opt/OpenFOAM/Open…  0B
7cb119e51ba1  17 hours ago  /bin/sh -c #(nop) COPY dir:db92694508b316ccc…  73.1kB
6e63df7efb1e  5 weeks ago                                                  2.23GB  Imported from -


docker save -o dummy_foam-f2fbf95.tar andreweiner/dummy_foam:f2fbf95
docker image rm andreweiner/dummy_foam:f2fbf95
docker image ls
...
docker load -i dummy_foam-f2fbf95.tar
docker image ls
...

Conclusion

Docker minimizes dependencies
Docker images are easy to share
Docker containers are always ready to use
Running a container with the same options will always give 100% identical results

More pros and cons you can think of?

THE END

Thank you! Let me know what you think!

Get in touch: weiner@mma.tu-darmstadt.de

Time for discussion ...