Singularity

See also: HPC and HTC tutorial | Run MPI On Grid'5000 | GPUs on Grid5000 | GNU Parallel | Modules | Conda | Guix | Singularity | Deep Learning Frameworks

	Note
	This page is actively maintained by the Grid'5000 team. If you encounter problems, please report them (see the Support page). Additionally, as it is a wiki page, you are free to make minor corrections yourself if needed. If you would like to suggest a more fundamental change, please contact the Grid'5000 team.

Singularity is a popular container solution for HPC systems. It natively supports GPU and high performance networks in containers and is compatible with docker images. Grid'5000 supports the Singularity containers. It is available using module and does not requires root privileges. More info at: https://sylabs.io/docs/.

Basic usage

Load singularity module :

node:

module load singularity

Just run the singularity command to use it :

node:

singularity run library://sylabsed/examples/lolcow

The Singularity user documentation is available at https://sylabs.io/guides/latest/user-guide. It describes the various ways to run programs inside a container and how to build your own container image.

Building a singularity image

Recent versions of Singularity allow building images without root access (see https://docs.sylabs.io/guides/latest/user-guide/fakeroot.html). However this has limitations, so it is better to build images as root. It can be performed on your own laptop or on a Grid'5000 node using "sudo-g5k" :

node:

module load singularity && sudo-g5k $(which singularity) build mpi.sif mpi.def

For more information about building Singularity containers, see https://docs.sylabs.io/guides/latest/user-guide/build_a_container.html

Using docker containers with Singularity

Singularity can also be used to start docker containers. For instance:

node:

singularity run docker://debian

Running singularity containers in OAR submission

Singularity containers can also be run in a OAR submission (none-interactive batch job). For instance:

frontend:

oarsub -l core=1 "module load singularity && singularity run library://sylabsed/examples/lolcow"

Running MPI programs in Singularity containers

MPI programs may be run in Singularity containers, by leveraging both the MPI implementation available in the host, i.e. a Grid'5000 physical node (which has a direct access to the high peformance network hardware if present), and the MPI library that must be installed inside the container.

MPI programs in the Singularity container can then be started using the the mpirun command on the host.

See https://sylabs.io/guides/latest/user-guide/mpi.html for more information.

For instance, to submit such a MPI job under OAR, assuming Singularity image named my_mpi_image.sif in your home directory, use:

frontend:

oarsub -l nodes=2 "module load singularity && mpirun -hostfile \$OAR_NODE_FILE --mca orte_rsh_agent oarsh -- `which singularity` exec my_mpi_image.sif /opt/mpitest"

Using GPUs in Singularity containers

GPUs available in the host can be made available inside the container by using the --nv option (for Nvidia GPUs only).

For instance, to start an interactive tensorflow environment with one GPU, first submit the job reserving 1 GPU:

frontend:

oarsub -I -l gpu=1

	Note
	You may need to add "-q production" or "-t exotic" depending which GPU cluster you want to use

Then on that node:

node:

module load singularity

node:

singularity run --nv docker://tensorflow/tensorflow:latest-gpu

More info at: https://sylabs.io/guides/latest/user-guide/gpu.html

Using Apptainer (instead of Singularity)

As Sylabs forked the Singularity project without renaming their fork, the Singularity project decided to move into the Linux Foundation and rename their project Apptainer. See the official announcement for more information.

As Singularity, Apptainer is available through module. To use it, just load the module and execute your container:

node:

module load apptainer

node:

apptainer run docker://alpine

Example: Using Singularity to port a software environment between HPC infrastructures

Using Singularity is a good way to port software environments between HPC infrastructures, for example, between Grid'5000 and IDRIS' Jean Zay.

The following example describes how Singularity could be used together with Conda to share your software environment on two different HPC infrastructures (it is inspired from this stackoverflow question).

Step 1 - On Grid'5000, create a Docker container with your Conda environment

(based on the micromamba Quick Start guide)

Create a env.yaml file to describe your Conda environment:

name: base
channels:
  - conda-forge
dependencies:
  - tensorflow-gpu

Create a Dockerfile:

FROM mambaorg/micromamba:latest
COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

Create a Docker image using this environment: (see Docker)

node:

g5k-setup-docker

node:

docker build --tag my_app .

Check your docker image:

node:

docker run -it --rm my_app python3 -c "import tensorflow as tf; print('Num GPUs Available:', len(tf.config.list_physical_devices('GPU')))"

Step 2 - On Grid'5000, convert your Docker image to a Singularity image

Export your Docker image:

node:

docker save -o my_app.tar my_app

Convert it to a Singularity image:

node:

singularity build my_app.sif docker-archive://my_app.tar

Test your Singularity image:

$ singularity shell --nv my_app.sif 
Singularity> eval "$(micromamba shell hook --shell bash)"
Singularity> micromamba activate
(base) Singularity> python -c "import tensorflow as tf; print('Num GPUs Available:', len(tf.config.list_physical_devices('GPU')))"
Num GPUs Available: 2
(base) Singularity>

Step 3 - Copy your Singularity image to Jean Zay (using scp/rsync) and run it there

Note that unless you added Grid'5000's external addresses to your IDRIS account as described in the FAQ, you must copy your image locally and then copy it to Jean Zay.

Specific information about running Singularity containers on Jean Zay is available at http://www.idris.fr/eng/jean-zay/cpu/jean-zay-utilisation-singularity-eng.html.

$ module load singularity
$ idrcontmgr cp my_app.sif 
1 file copied.
$ singularity shell --nv $SINGULARITY_ALLOWED_DIR/my_app.sif 
Singularity> eval "$(micromamba shell hook --shell bash)"
Singularity> micromamba activate
(base) Singularity> python -c "import tensorflow as tf; print('Num GPUs Available:', len(tf.config.list_physical_devices('GPU')))"
Num GPUs Available: 1
(base) Singularity>