Mat3ra application containers (public)

This repository contains Apptainer (Singularity) definitions of Mat3ra public application containers. Containers are built automatically via GitHub workflow and are hosted on GitHub Container Registry.

Managing ENV variables

Apptainer manages ENV variables with a number of shell scripts under /.singularity.d/env:

# ls -l /.singularity.d/env
total 10
-rwxr-xr-x 1 root root 1337 Aug  1 01:32 01-base.sh
-rwxr-xr-x 1 root root   85 Aug  1 01:32 10-docker2singularity.sh
-rwxr-xr-x 1 root root 1707 Dec  6 06:18 90-environment.sh
-rwxr-xr-x 1 root root    0 Dec  6 06:09 94-appsbase.sh
-rwxr-xr-x 1 root root 3052 Aug  1 01:32 95-apps.sh
-rwxr-xr-x 1 root root 1568 Aug  1 01:32 99-base.sh
-rwxr-xr-x 1 root root  922 Aug  1 01:32 99-runtimevars.sh

90-environment.sh is where the variables from %environment definition goes. Above files are generated every time a new container is built, they are not preserved from the base images. However, if we write variables to any other file under /.singularity.d/env, they are preserved and sourced in runtime. Notice the numerical prefix, that determines the order of sourcing. We can write custom ENV variables to $APPTAINER_ENVIRONMENT in the %post section, it will save them to 91-environment.sh. This file will be sources runtime automatically, if we need these variables runtime, we can source manually:

if [ -f /.singularity.d/env/91-environment.sh ]; then
    . /.singularity.d/env/91-environment.sh
fi

1. Write ENV variables to $APPTAINER_ENVIRONMENT in base images.

echo 'export ONEAPI_ROOT=/opt/intel-2023.1' >> $APPTAINER_ENVIRONMENT

or

cat >> $APPTAINER_ENVIRONMENT <<'EOF'
export ONEAPI_ROOT=/opt/intel-2023.1
export TBBROOT=$ONEAPI_ROOT/tbb/2021.11
EOF

Notice the single quote above to preserve the bash variables in echo or cat output, and substitute them runtime.

2. Set application container (final container) ENV variables via %environment definition.

Links

• https://apptainer.org/docs/admin/latest/