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


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.



What is Shifter ?

Shifer allows to use Docker images in a shared computing environment in userland. It converts the docker image to the squashfs format that can be mounted and chrooted into as a user.

The SCITAS filesystems are also mounted inside the image so you can easily access your data. Please note that if your image has some files in /home there will not appear in the image and will be hidden.


You can use public images without being authenticated (shifterimg login) in the following cases:

Image sourcePublic imageLogin required
DockerhubNoYes, Dockerhub
C4science registryYes


C4science registryNoYes, c4science registry

When using authentication, it's relative to the source you want to use (Dockerhub and c4science registry supported) and the authentication is saved per cluster.

You need to ask for an account on the c4science registry, see Account request.

NOTE: By defaut, shiterimg is pulling from c4science registry, you have to specify for Dockerhub

Upload an image to Shifter from Dockerhub using the (preferred)


You need to have Docker installed on your machine

  1. Get a docker image from dockerhub Dockerhub for instance (From local computer)

    Code Block
    $ docker pull alpine:latest
    $ docker images

  2. Account on the c4science registry
  3. Request an account
  4. Change your password on
    Set up your machine (From local computer)

    Login on the registry from your local Docker installation (you need an account, see Account request)

    Code Block
    $ docker login
    Username (username): username
    Login Succeeded

  5. Upload a Docker image to the registry (From local computer)

    • 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
      NOTE: Do not use the `-` character in the tag name, only letters, numbers and underscore

      Code Block
      $ docker tag alpine:latest
      $ docker push

  6. Pull an image on Shifter and specify a user or group ACL (From cluster login node)

    • From a each cluster frontend (i.e.:, login to the registry, pull the image and check it's was pulled OKwith success.

      Code Block
      $ 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

      Code Block
      $ id
      $ shifterimg --group scitas-ge --user aubort,user2 pull yourproject/alpin

    • To update the user/group ACL you can re-run the pull command
    • The images are unique for each cluster (deneb, fidis, helvetios, izar)
    • To view the full info about the images (warning: JSON):

      Code Block
      $ shifterimg -v images
      Message: {
        "list": [
            "ENTRY": null, 
            "ENV": [
            "WORKDIR": "MISSING", 
            "groupACL": [], 
            "id": "9797e5e798a034d53525968de25bd25c913e7bb17c6d068ebc778cb33e3ff6e5", 
            "itype": "docker", 
            "last_pull": 1536842228.15727, 
            "status": "READY", 
            "status_message": "", 
            "system": "fdata2-int.fidis", 
            "tag": [
            "userACL": []

Upload an image directly from Dockerhub to Shifter

Optional (needed for private images only)

Code Block
$ shifterimg login

Get the image from Dockerhub by specifying the image account (optional for official image) and name

Code Block
$ shifterimg pull
# OR
$ shifterimg pull

$ shifterimg images
fidis      docker     READY    4a28aef4f8   2020-10-16T14:52:41
fidis      docker     READY    d0877b767c   2020-09-16T15:26:31

$ srun --pty -p debug -N 1 shifter --image /bin/sh
~ $ cat /etc/alpine-release 

Run the image on the clusters

You can submit the following Slurm script with the sbatch command


On Deneb shifter runtime is installed on the GPU nodes. You need prior access to the GPUs nodes, see FAQ

Code Block
[aubort@deneb1 ~]$ srun --gres gpu:1 --partition gpu --qos gpu shifter --image library/debian:stable-slim nvidia-smi -L
GPU 0: Tesla K40m (UUID: GPU-21730043-7144-85e7-d251-7834adb2d1ee)

[aubort@deneb1 ~]$ srun --gres gpu:1 --partition gpu --qos gpu shifter --image library/nvidia-cuda:9.1-runtime /home/aubort/gpu/cuda-samples/bin/x86_64/linux/release/simpleCUFFT 
[simpleCUFFT] is starting...
GPU Device 0: "Tesla K40m" with compute capability 3.5

Temporary buffer size 448 bytes
Transforming signal cufftExecC2C
Launching ComplexPointwiseMulAndScale<<< >>>
Transforming signal back cufftExecC2C

FEEDBACK is welcome as this feature is experimental.

Account on the c4science registry

Content by Label
cqllabel in ("slurm","docker","shifter") and type = "page" and space = "DOC"
labelsslurm shifter docker