Skip to content

apptainer.md

Latest commit

 

History

History
32 lines (24 loc) · 1.49 KB

apptainer.md

File metadata and controls

32 lines (24 loc) · 1.49 KB

Apptainer

For a detailed explanation of how to use Apptainer on SDF, you can go through Yee-Ting Li's presentation here where you can find both the slides and the zoom recording.

Prerequisite

As pulling and building a new image can use quite a lot of disk space, we recommend that you set the appropriate cache paths for apptainer to not use your $HOME directory. Therefore, before pulling or building an image, define the following environment variables:

export DIR=${LSCRATCH}/.apptainer
mkdir -p $DIR
export APPTAINER_LOCALCACHEDIR=$DIR
export APPTAINER_CACHEDIR=$DIR
export APPTAINER_TMPDIR=$DIR

Pulling images

To pull an image from DockerHub, do:

apptainer pull docker://<user or organization>/<repository>:<tag>

Miscellaneous

By default apptainer overrides your terminal prompt with Apptainer> in order to emphasize that you are opening a terminal within a container. If you prefer a less stark reminder you may instead include the following lines in ~/.bashrc for a more familiar prompt with a subtler (apptainer) prefix indicating the environment is within a container.

# add a prefix if this shell is in a container
export PROMPT_COMMAND='[ -f /singularity ] && PS1="(apptainer) ${PS1}"; unset PROMPT_COMMAND'

This would make the terminals that you open in Jupyter Lab appear with your customary prompt, except for the additional (apptainer) prefix.