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

Running a Docker image with Shifter - Step by step

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
  3. Upload a Docker image to the registry

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

  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
 
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


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