Hi Samy,
to overwrite an environment variable, you could force it by modifying
Singularity's container actions.
I.e.,
use a temporary variable to track the host's LD_LIBRARY_PATH and add an
export to an action script for example, which replaces the
LD_LIBRARY_PATH in the container's context with the temporary one.
For the shell action, something like
%post
sed -i '1iexport LD_LIBRARY_PATH=${MYOUTERPATH}'
/.singularity.d/actions/shell
should work when building the container (same for exec, run, start,test)
before running your container, you would then have to copy your path
into the tmp var
SINGULARITYENV_MYOUTERPATH=${LD_LIBRARY_PATH}
singularity shell your.container
However, that would require, that your container is more or less
equivalent with your host environment - else all your shared libraries
will clash.
Cheers,
Thomas
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