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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


Account on the c4science registry

Set up your machine

  • Login on the registry from your local Docker installation

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

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:latest

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

    $ id
    $ shifterimg --group scitas-ge --user aubort,user2 pull yourproject/alpine

  • 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:latest

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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