Connecting to Singularity/Apptainer Containers
The following contains a guide how to actively develop in a Singularity/Apptainer container. See Singularity/Apptainer for more information on the singularity module. Both Singularity and Apptainer are largely compatible with each other, and in fact you run the container with the singularity command regardless of which module you use.
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This guide was contributed by our GPU users Anwai Archit and Arne Nix who kindly provided this documentation. It is lightly edited to fit the format of this page and fix a few typos. Any place you see "singularity", you could replace it with "apptainer" if you use the apptainer module instead. It was written for the Grete GPU nodes of Emmy, but can be easily translated to other partitions/clusters (see /wiki/spaces/PUB/pages/428683 for more information). Obviously, rename any directories and files as makes sense for your user name, the SIF container file you use, and the names of your files and directories.
Starting a Singularity Container
First we need to setup a singularity container and submit it to run on a GPU node. For me this is done by the following SBATCH script:
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- We need to load
cudaandsingularityto have it available to our container. - We need to bind
$HOME/.vscode-serverto the same place in the container. - We need to remember the name of our container. In this case:
anix_dev-0 - We need to keep the script running in order to not loose the node. This is achieved by
sleep infinity.
SSH Config to Connect to the Container
We want to connect to the container via ssh. For this, setup the following configuartion in ~/.ssh/config on your local machine.
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- Connection to the login node:
ssh hlrn - Connection to a compute node that we obtained through the scheduler, e.g.
ssh hlrn-ggpu02 - Connection to the singularity container running on a compute node, e.g.
ssh hlrn-ggpu02-singularity
Connecting VS-Code to the Container
This follows mostly the tutorial here. Then add the following lines:
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