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When you want to run Docker containers on the Fidis/Gacrux cluster

Warning

We are still in beta phase. The installation will soon be improved with:

  • automatic account creation on the registry

The present documentation will be updated once the registry has been modified.


Step-by-step guide


Prerequisite

You need to have Docker installed on your machine and a local docker image.

To see the images available on your machine, use the command


docker images


  1. Account on the c4science registry

  2. Set up your machine

    • Login on the registry from your local Docker installation

      $ docker login registry.c4science.ch
Username (username): username
Password: 
Login Succeeded

  3. Upload a Docker image to the registry

    • On the web interface, create a Project on the registry (private or public)

    • Tag the image you want to upload on your local machine and push it to the registry

      $ docker tag alpine:latest registry.c4science.ch/yourproject/alpine:latest
$ docker push registry.c4science.ch/yourproject/alpine:lates

  4. Pull an image on Shifter and specify a user or group ACL

    • From the frontend, pull the image

      $ shifterimg login
default username: username
default password:
$ shifterimg pull yourproject/alpine:latest
$ shifterimg images
tcm        docker     READY    9797e5e798   2018-03-15T16:00:59 yourproject/alpine:latest

    • You can specify one or multiple (separated by a comma) LDAP username and/or group so the image is only available to those people

      $ id
$ shifterimg --group scitas-ge --user aubort,user2 pull yourproject/alpin
    • To update the user/group ACL you can re-run the pull command

    • To view the full info about the images (warning: JSON):

      $ shifterimg -v images
tcm        docker     READY    9797e5e798   2018-03-15T16:00:59 yourproject/alpine:lates
  5. Run the image

You can submit the following Slurm script with the sbatch command

#!/bin/bash -l
 
#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 1024
#SBATCH --image yourproject/alpine
 
sleep 10
 
shifter ls /etc
 
sleep 10

 



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