Remark
This section summarize what we have done at the University of Oslo to install docker and build our containers. It is not intented to explain you in details how containers work. For a more complete introduction on docker, we suggest to follow the Carpentries incubator lesson Reproducible computational environments using containers
To test and run our docker containers, we use IaaS and create a virtual machine with centos-7. Then we install docker using the following instructions:
sudo yum check-update
curl -fsSL https://get.docker.com/ | sh
sudo usermod -aG docker centos
sudo systemctl start docker
sudo systemctl status docker
It allows to start docker automatically when the machine is rebooted
sudo systemctl enable docker
The default disk on our Virtual Machine is about 20GB e.g. too small for our docker images so we create a new volume /opt/uio/ (500GB).
First create a new volume and attach it to your Virtual Machine.
Then change default folder to /opt/uio/docker:
sudo mkdir /opt/uio/docker
You should have:
ls -lrt
drwx--x--x. 14 root root 4096 Nov 2 10:25 docker
And then change the default location to this new folder:
sudo systemctl stop docker
Then edit (with sudo) sudo vi /etc/docker/daemon.json and add:
{
"data-root": "/opt/uio/docker"
}
Finally restart docker:
sudo systemctl start docker
Logout and login again (to make sure centos username is part of docker group).
docker ps
This command should return:
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
0
docker info
It should return something like:
Client:
Debug Mode: false
Server:
Containers: 1
Running: 1
Paused: 0
Stopped: 0
Images: 21
Server Version: 19.03.4
Storage Driver: overlay2
Backing Filesystem: extfs
Supports d_type: true
Native Overlay Diff: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
Volume: local
Network: bridge host ipvlan macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: b34a5c8af56e510852c35414db4c1f4fa6172339
runc version: 3e425f80a8c931f88e6d94a8c831b9d5aa481657
init version: fec3683
Security Options:
seccomp
Profile: default
Kernel Version: 3.10.0-1062.4.1.el7.x86_64
Operating System: CentOS Linux 7 (Core)
OSType: linux
Architecture: x86_64
CPUs: 32
Total Memory: 117.9GiB
Name: hpc32.novalocal
ID: XNRD:EARM:KHVU:ZH47:QS32:NBE2:FHYX:MGW7:GMLK:RNIK:KT36:2J4D
Docker Root Dir: /opt/uio/docker
Debug Mode: false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
127.0.0.0/8
Live Restore Enabled: false
docker ps --filter "status=exited"
Then stop and rm your container id:
docker stop <container_id>
and
docker rm <container_id>
docker images
The command above allows you to get the image identifier. Now you can remove your image with the following command:
docker rmi <image_id>