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fix running command as 'easybuild' user in generated Singularity definition file #3347

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merged 2 commits into from
May 25, 2020

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@boegel boegel commented May 25, 2020

fixes #3171

Switching to another user no longer works, and after consulting with the Singularity developers it seems this was actually working by accident in earlier versions of Singularity.

As an alternative, we run a set of commands as the easybuild user by using a here document.

The quoted 'EOF' is important to ensure that $LMOD_DIR does not get resolved too early, which leads to a confusing error like:

/update_lmod_system_cache_files -d /app/lmodcache -t /app/lmodcache/timestamp /app/modules/all
-bash: line 28: /update_lmod_system_cache_files: No such file or directory
FATAL:   failed to execute %post proc: exit status 1

@boegel boegel added the bug fix label May 25, 2020
@boegel boegel added this to the next release (4.2.2?) milestone May 25, 2020
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singularity def issue with switching to easybuild user to build eb package
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