Singularity on the SCC

Singularity is a containerization system focused on scientific needs and designed for running on HPC resources. At GWDG Singularity can be used by simply loading the corresponding module:

module load singularity

After the module is loaded you are ready to pull and run your containers. In difference to Docker you can provide your own container images.

For building you can use Docker images or Singularity bootstrap files. You can find the documentation for a building process at https://sylabs.io/docs/.

Examples

Several examples of Singularity usecases will be shown below.

Jupyter and IPython Parallel with Singularity

As an example we will pull and deploy the Singularity image containing Jupyter and IPython Parallel.

First create a new folder in your $HOME directory. After that go to the directory and pull a container using Docker or Singularity registries or upload a locally built image. Here we will use a public Singularity image from SingularityHub, shub://A33a/sjupyter. Because SingularityHUB builds images automatically this takes time. If you want to have your container more quickly, then either build it locally, or load it into the DockerHub.

For pulling the image run the following command:

singularity pull --name sjupyter.simg shub://A33a/sjupyter

Now the sjupyter.simg image is ready to be containerized. To submit the corresponding job, run the command:

srun --pty -p int singularity shell sjupyter.simg

Here we are requesting a shell to the container in the interactive partition.

GPU access within the container

GPU devices are visible within the container by default. Only driver and necessary libraries should be installed or binded to the container. You can install Nvidia drivers yourself or bind it to the container. To bind it automatically you need to run the container with --nv flag. For instance singularity shell --nv sjupyter.simg. If you want to use specific version of the driver you can install it within the container or link existing version of a driver provided by the cluster to the container. For drivers to be visible inside the container, you have to add their location to environment variable LD_LIBRARY_PATH. Here is example of linking Nvidia driver version 384.111:

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/cm/local/apps/cuda-driver/libs/384.111/lib64

When running a conitainer the corresponding path should be binded to it with -B option:

singularity shell -B /cm/local/apps jupyterCuda.simg

The libraries like CUDA and CuDNN should be mentioned in LD_LIBRARY_PATH variable as well:

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/cuda-9.0/lib64

Here we have CUDA v9.0 installed within the container at /usr/local/cuda-9.0

If you want to use nvidia-smi command, then add its location to PATH environment variable. In the cluster we have it at /cm/local/apps/cuda/libs/current/bin:

export PATH=${PATH}:/cm/local/apps/cuda/libs/current/bin

The example below is Singularity container bootstrap file which can be used for building the container based on Nvidia Docker image with preinstalled CUDA v9.0 and CuDNN v7 on Ubuntu 16.04 (more images of Nvidia can be found on DockerHub). As an example we install here a GPU version of tensorflow. Also the container uses current Nvidia drivers installed in the GWDG cluster:

Bootstrap: docker
From: nvidia/cuda:9.0-cudnn7-runtime

%post

apt-get -y update
apt-get -y install python3-pip

pip3 install --upgrade pip
pip3 install tensorflow-gpu 

%environment

PATH=${PATH}:${LSF_BINDIR}:/cm/local/apps/cuda/libs/current/bin
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/cuda-9.0/lib64:/cm/local/apps/cuda-driver/libs/current/lib64
CUDA_PATH=/usr/local/cuda-9.0
CUDA_ROOT=/usr/local/cuda-9.0

You can shell into the container with:

singularity shell -B /cm/local/apps CONTAINERNAME.simg