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When you want to run Docker containers on the clusters.

Authentication

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

Image sourcePublic imageLogin required
DockerhubYesNo
DockerhubNoYes, dockerhub
C4science registryYes

No

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.

Upload an image to Shifter from dockerhub using the registry.c4science.ch (preferred)

Prerequisite

You need to have Docker installed on your machine

  1. Get a docker image from dockerhub for instance

    $ docker pull alpine:latest
    $ docker images
  2. Set up your machine

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

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

      $ docker tag alpine:latest registry.c4science.ch/yourproject/alpine:latest
      $ docker push registry.c4science.ch/yourproject/alpine:latest
  4. Pull an image on Shifter and specify a user or group ACL

    • From each cluster frontend (i.e.: fidis.epfl.ch), login to the registry, pull the image and check it's was pulled with success.

      $ 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
    • The images are unique for each cluster (deneb, fidis, helvetios, izar)
    • To view the full info about the images (warning: JSON):

      $ shifterimg -v images
      Message: {
        "list": [
          {
            "ENTRY": null, 
            "ENV": [
              "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
            ], 
            "WORKDIR": "MISSING", 
            "groupACL": [], 
            "id": "9797e5e798a034d53525968de25bd25c913e7bb17c6d068ebc778cb33e3ff6e5", 
            "itype": "docker", 
            "last_pull": 1536842228.15727, 
            "status": "READY", 
            "status_message": "", 
            "system": "fdata2-int.fidis", 
            "tag": [
              "scitas/alpine:latest"
            ], 
            "userACL": []
          },
      [...]

Upload an image directly from dockerhub to Shifter

Optionnal (for private dockerhub images)

$ shifterimg login registry-1.docker.io

Get the image from dockerhub by specifying the image account (optionnal for official image) and name

$ shifterimg pull registry-1.docker.io/alpine:latest
# OR
$ shifterimg pull registry-1.docker.io/library/alpine:latest

$ shifterimg images
fidis      docker     READY    4a28aef4f8   2020-10-16T14:52:41 registry-1.docker.io/alpine:latest
fidis      docker     READY    d0877b767c   2020-09-16T15:26:31 registry-1.docker.io/library/busybox:latest

$ srun --pty -p debug -N 1 shifter --image registry-1.docker.io/alpine:latest /bin/sh
~ $ cat /etc/alpine-release 
3.12.0

Run the image on the clusters

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
 
srun shifter --image yourproject/alpine ls /etc

Interactive Shell (Bash)

To have an interactive shell within your image, simply use this:

$ srun --pty shifter --image yourproject/alpine bash

Using GPUs

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

[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