Containers cheat sheet

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Revision as of 07:28, 23 February 2021 by hpcwiki>Dvory
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action docker singularity
pull existing image from docker hub
docker pull ubuntu:18.04
sudo singularity build ubuntu_18.04.simg docker://ubuntu:18.04
login to container shell
docker run -it ubuntu:18.04 bash
singularity shell ubuntu_18.04.simg
update image NOT using a file Login to container shell:
docker run -it ubuntu:18.04 bash
apt update
apt install vim
exit

Commit the changes while the container is down:

Locate Container ID:
docker ps -a
Commit the changes to a new image tag:
docker commit 19b0acbfef1b ubuntu:18.04_tau
Create writable image:
sudo singularity build --sandbox ubuntu_18.04_tau.simg docker://ubuntu:18.04
Login to image shell in a writable mode:
sudo singularity shell --writable ubuntu_18.04_tau.simg
apt update
apt install vim
exit
create new image 1. Edit Dockerfile (file name must be Dockerfile):
#Download base image
FROM ubuntu:18.04
# Update vim
RUN apt update && apt install -y vim
# Define environment variable
ENV TEAM HPC

2. Build image:

 docker build -t ubuntu:18.04_tau2 .

1. Edit Singularity file (file name can be anything):

#Download base image
Bootstrap: docker
FROM: ubuntu:18.04
# Update vim
%post
  apt-get update
  apt-get install -y vim
%environment
  TEAM=HPC
  export TEAM

2. Build image:

sudo singularity build ubuntu_18.04_tau2.simg Singfile
run as a daemon Run image as daemon using infinite sleep:
docker run -d ubuntu:18.04_tau2 sleep 999999999
list running containers
docker ps
list running and stopped containers
docker ps -a
list local images
docker images
ls
Start a downed container (note it must have already been executed at least once)
docker start c4f7efb53d1a
Stop a container
docker stop c4f7efb53d1a
Delete a container
docker rm 3271c613e00a
Delete an image
docker rmi 9f38484d220f
rm ubuntu_18.04_tau2.simg
view container logs
docker logs f28eb1af539d
view disk usage
docker system df
view full details about the docker service
docker info
view full details about a container
docker inspect containerid
start shell inside daemonized container
docker exec -it f28eb1af539d bash
To exit: <CTL>+p, <CTL>+q (typing 'exit' will kill the container)
Run program from within the image without parameters
docker run -it ubuntu:18.04_tau4 python
Add to the Singularity file:
%apprun python
  exec python ""${@}""

Build the singularity image:

sudo singularity build ubuntu_18.04_tau2.simg Singfile

Run the program:

singularity run --app python ubuntu_18.04_tau4.simg
Run program from within the image with parameters
docker run -it ubuntu:18.04_tau4 python -c "print('hello world')"
Add to the Singularity file:
%apprun python
  exec python "${@}"
Build the singularity image:
sudo singularity build ubuntu_18.04_tau2.simg Singfile
Run the program:
singularity run --app python ubuntu_18.04_tau4.simg -c "print('hello world')"
Add help to image Add to the Singularity file:
%help
  Python version 2.7.15rc1
 
  Usage
  =====
  View help: 
    $ singularity help ubuntu_18.04_tau4.simg 
  Run Python from the container: 
    $ singularity run --app python ubuntu_18.04_tau4.simg
Build the singularity image:
sudo singularity build ubuntu_18.04_tau2.simg Singfile
View the help:
singularity help ubuntu_18.04_tau4.simg