GPU builds in EESSI container are broken with Apptainer 1.5.0

[bedroge]

Apptainer 1.5.0 automatically adds system library locations to $LD_LIBRARY_PATH if host libraries are bind mounted to /.singularity/libs (which is done for the --nv flag, i.e. for GPU builds), see https://github.com/apptainer/apptainer/blob/main/CHANGELOG.md#changed-defaults--behaviours. This breaks our startprefix script, as it will pick up the glibc from the host:

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/bin/bash: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/bin/bash)


Apptainer> echo $LD_LIBRARY_PATH
/usr/lib/x86_64-linux-gnu/libfakeroot:/usr/local/lib:/lib/x86_64-linux-gnu:/lib:/.singularity.d/libs

Older versions did not do this, they would only set:

Apptainer> echo $LD_LIBRARY_PATH
/.singularity.d/libs

[bedroge]

Possible workaround:

APPTAINERENV_LD_LIBRARY_PATH=/.singularity.d/libs

This overrides the container's $LD_LIBRARY_PATH, and basically results in the same behavior as with older versions.

[ocaisa]

This could also be "solved" with #114 in a more bullet-proof way