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
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