1.1. Introduction
Containerization is a method to isolate computing environment (operating system, data, software, configurations, etc.) into reusable packages called images. These are binary files which can easily be transferred between different machines. Images are instantiated into running Containers by a Container Engine. From user perspective, working with the Container is similar to working with another operating system on the shared hardware resources. This resembles what Virtual Machines provide. However, there are important technical differences between Container and Virtual Machine technologies. Mainly, any number of Containers can be executed by a single Container Engine on a single operating system. In case of Virtual Machines, each runs its own operating system with its own layer of hardware abstraction. In consequence, Containers are in general quicker to start and easier to operate.
1.2. Docker
The main Containerization technology used now is Docker. It consists of image file format description, the Container Engine and other components. It is available for Linux, macOS and Windows.
For more information, check Get Started
1.3. uDocker
uDocker is "a basic user tool to execute simple docker containers in user space without requiring root privileges".
For more information, check indigo-dc/udocker
1.4. Docker vs uDocker
Important: While uDocker has mostly identical commands and parameters as Docker, there are some minor differences:
- Docker:
docker create
: prepare a container from an imagedocker start
: start a prepared containerdocker run
: prepare a new container and start it in a single stepdocker exec
: execute commands on a started container
- uDocker:
udocker create
: prepare a container from an imageudocker run
: execute commands on an existing container or prepare a new container and execute command on it- There is no
udocker start
andudocker exec
!
In consequence, the typical usage for Docker is combination of docker run
and optionally docker exec
. For uDocker, the typical usage is a combination of udocker create
and udocker run
.
Please be aware not to mix these usage scenarios.
uDocker is slower to prepare a container, so incorrect usage of udocker run
may end up in starting multiple containers and each operation taking a long time.
1.5. Goal
The goal of IMAS Docker creation is to prepare a Docker image containing full IMAS environment with additional tools such as Kepler and FC2K.
1.6. Latest IMAS Docker image
- IMAS version: 3.20.0
- UAL version: 3.8.3
- Kepler present
- FC2K not present yet
- Available on the Gateway:
~g2tomz/public/imas-installer-20180921112143.tar.xz
1.7. Preparing uDocker on Gateway
mkdir -p ~/.local/bin $ITMWORK/dot-udocker ln -s $ITMWORK/dot-udocker ~/.udocker curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py > ~/.local/bin/udocker chmod u+rx ~/.local/bin/udocker echo "tmpdir='$ITMSCRATCH'" > ~/.udocker/udocker.conf ~/.local/bin/udocker install
1.8. Loading Docker image
Docker on your own compujter:
scp login.eufus.eu:~g2tomz/public/imas-installer-20180921112143.tar.xz ./ xzcat imas-installer-20180921112143.tar.xz | docker load
uDocker on Gateway:
xzcat ~g2tomz/public/imas-installer-20180921112143.tar.xz | ~/.local/bin/udocker load
1.9. Demonstration 1: Python script
Create a container and start a shell in it:
Docker on your own computer:
docker run --interactive --tty --name imas imas-installer:20180921112143
uDocker on Gateway:
~/.local/bin/udocker create --name=imas imas-installer:20180921112143 ~/.local/bin/udocker run imas
In the container shell, execute:
module load imas imasdb test python /home/imas/imas-installer/src/$IMAS_VERSION/ual/$UAL_VERSION/examples/dd-v3/python/put_pf.py
On the host machine, execute:
docker cp imas:/home/imas/public/imasdb/test/3/0/ids_120001.characteristics /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_120001.datafile /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_120001.tree /tmp/
Transfer the generated IDSes to the Gateway:
scp /tmp/ids_120001.* login.eufus.eu:public/imasdb/test/3/0/
1.10. Demonstration 2: Kepler workflow
Start a new Docker container
docker run --interactive --tty --name imas imas-installer
In the container shell, execute:
module load imas kepler module load keplerdir imasdb test export USER=imas kepler -runwf -nogui -user imas /home/imas/simple-workflow.xml
On the host machine, execute:
docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.characteristics /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.datafile /tmp/ docker cp imas:/home/imas/public/imasdb/test/3/0/ids_10001.tree /tmp/
Transfer the generated IDSes to the Gateway:
scp /tmp/ids_10001.* login.eufus.eu:public/imasdb/test/3/0/
a basic user tool to execute simple docker containers in user space without requiring root privileges