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.

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. Account on the c4science registry
  3. Set up your machine
  4. Upload a Docker image to the registry

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

  6. 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.


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