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Creating containers

CSC's supercomputers Puhti and Mahti support running Apptainer containers (formerly known as Singularity). If you wish to run a container-based application, first check the application pages to see if a pre-installed container is already available. Also see our documentation on how to run containers.

If you cannot find a pre-built container, one option is to build your own. If a Docker container image already exists, you can often simply convert that to an Apptainer container. Another option is to build your own container from scratch. Both approaches will be discussed below. As always, if you have any problems or questions, don't hesitate to contact CSC's Service Desk.

Converting a Docker container

If you already have an existing Docker container, in many cases it can easily be converted to an Apptainer image. Docker container images can be found in public repositories such as Docker Hub, but please take care to only use images uploaded from reputable sources as these images can easily be a source of security vulnerabilities or even contain malicious code.

GPU-optimized containers can also be found in NVIDIA's GPU cloud (NGC). These containers have been prepared by NVIDIA, and should thus be safe.

Further information about converting Docker containers can be found in the Apptainer documentation.

Here is an example of how to build an Apptainer image on Puhti from NVIDIA's PyTorch Docker image. We'll use sinteractive as heavy processing should not be done in the login nodes.

# Let's start a 1 hour interactive job with enough memory and local scratch space
sinteractive --account <project> --time 1:00:00 -m 16G --tmp 64

# Let's use the fast local drive for temporary storage
export APPTAINER_TMPDIR=$LOCAL_SCRATCH
export APPTAINER_CACHEDIR=$LOCAL_SCRATCH

# This is just to avoid some annoying warnings
unset XDG_RUNTIME_DIR

# Change directory to where you wish to store the image
cd /projappl/<project>

# Do the actual conversion
# NOTE: the Docker image is downloaded straight from NGC
apptainer build pytorch_22.09-py3.sif docker://nvcr.io/nvidia/pytorch:22.09-py3

Note that the Apptainer image .sif files can easily be several GB in size, so they should not be stored in your home directory, but for example in the project application directory projappl.

Also see our documentation on how to run containers.

Build a container from scratch

You can also build your own container from scratch. This is an option for more experienced users, and your main source of information is the official Apptainer documentation on building containers.

You can find some help also by looking at our tutorial on building Apptainer containers from scratch.


Last update: October 18, 2022