Specifying --env-file returns a UID / GID readonly warning

[jmmaljaars]

Version of Singularity

singularity-ce version 3.10.2-bionic

Describe the bug

Whenever I attempt to pass environment variables to a singularity container using the --env-file option, the following warning is issued:

GID: readonly variable
UID: readonly variable

even if the --env-file is actually empty.

To Reproduce
Steps to reproduce the behavior:

1. create a file containing the environment variables as key-value pairs, see https://docs.sylabs.io/guides/3.7/user-guide/environment_and_metadata.html#env-file-option , e.g.

echo MY_VAR=host_var > .env

2. get an interactive singularity session, e.g.

singularity shell --env-file .env $SINGULARITY_CONTAINER

in which the $SINGULARITY_CONTAINER points to a valid .sif file.

Results in:

GID: readonly variable
UID: readonly variable
Singularity> echo $MY_VAR 
host_var

i.e. the variable is passed correctly, but I get an annoying GID / UID warning.

Expected behavior
I didn't expect the UID/GID readonly variable warnings.

OS / Linux Distribution
Which Linux distribution are you using?

Ubuntu 18.04.6 LTS

Installation Method
Installed by sysadmin, not sure which method he followed.

[dtrudg]

I'm afraid that this is not a bug, and is expected behaviour.

Specific environment variables are set readonly by the shell. You cannot modify them directly. Because singularity uses a shell interpreter to handle environment variables, the warnings you see are expected.

The same can be seen if you try to set UID or GID directly on your host's bash shell:

03:45 pm $ UID=abc
bash: UID: readonly variable

edit - actually maybe I am confused here... you are getting the warning with any --env-file, not just ones containing UID / GID? What SINGULARITYENV_ variables are set?

[dtrudg]

Okay - sorry... I replied to quickly there, with a misunderstanding. This does appear to be a bug.

[jmmaljaars]

I'm afraid that this is not a bug, and is expected behaviour.

Specific environment variables are set readonly by the shell. You cannot modify them directly. Because singularity uses a shell interpreter to handle environment variables, the warnings you see are expected.

The same can be seen if you try to set UID or GID directly on your host's bash shell:

03:45 pm $ UID=abc
bash: UID: readonly variable

edit - actually maybe I am confused here... you are getting the warning with any --env-file, not just ones containing UID / GID? What SINGULARITYENV_ variables are set?

Indeed, get this warning with any --env-file, even if the file itself is actually empty / trivial (i.e. definitely not containing UID, or GID as keys). Also,

printenv | grep SINGULARITYENV

is empty.

[dtrudg]

@jmmaljaars - this has been fixed in the main branch, and will be in the future 3.11 release. Thanks for the report.