UnicodeDecodeError on conda init

[WulfHans]

When trying a fresh setup, conda init fails with:

rschwa@leander:/home/stud/rschwa$ conda init --all

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/cli/main.py", line 83, in main_subshell
        exit_code = do_call(args, parser)
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 196, in do_call
        result = getattr(module, func_name)(args, parser)
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/cli/main_init.py", line 155, in execute
        return initialize(
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/core/initialize.py", line 137, in initialize
        run_plan(plan2)
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/core/initialize.py", line 798, in run_plan
        result = globals()[step["function"]](
      File "/home/stud/rschwa/miniforge/lib/python3.10/site-packages/conda/core/initialize.py", line 1454, in init_sh_user
        rc_content = fh.read()
      File "/home/stud/rschwa/miniforge/lib/python3.10/codecs.py", line 322, in decode
        (result, consumed) = self._buffer_decode(data, self.errors, final)
    UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 313: invalid continuation byte

`$ /home/stud/rschwa/miniforge/bin/conda init --all`

  environment variables:
                 CIO_TEST=<not set>
               CONDA_ROOT=/home/stud/rschwa/miniforge
           CURL_CA_BUNDLE=<not set>
                 INFOPATH=/opt/software/gcc/gcc-11.2.0/share/info:
          LD_LIBRARY_PATH=/opt/software/gcc/gcc-11.2.0/lib:/opt/software/gcc/gcc-11.2.0/lib64:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/software/gcc/gcc-11.2.0/share/man:
                NODE_PATH=/usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript
                     PATH=/home/stud/rschwa/miniforge/bin:/home/stud/rschwa/miniforge/bin:/opt/s
                          oftware/gcc/gcc-
                          11.2.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/a
                          fs/tu-chemnitz.de/home/urz/r/rschwa/:/afs/tu-
                          chemnitz.de/home/urz/r/rschwa/bin:/afs/tu-
                          chemnitz.de/home/urz/r/rschwa/:/afs/tu-
                          chemnitz.de/home/urz/r/rschwa/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : None
       user config file : /afs/tu-chemnitz.de/home/urz/r/rschwa/.condarc
 populated config files : /home/stud/rschwa/miniforge/.condarc
          conda version : 24.1.2
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=haswell
                          __conda=24.1.2=0
                          __glibc=2.24=0
                          __linux=4.9.0=0
                          __unix=0=0
       base environment : /home/stud/rschwa/miniforge  (writable)
      conda av data dir : /home/stud/rschwa/miniforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/stud/rschwa/miniforge/pkgs
                          /afs/tu-chemnitz.de/home/urz/r/rschwa/.conda/pkgs
       envs directories : /home/stud/rschwa/miniforge/envs
                          /afs/tu-chemnitz.de/home/urz/r/rschwa/.conda/envs
               platform : linux-64
             user-agent : conda/24.1.2 requests/2.31.0 CPython/3.10.14 Linux/4.9.0-8-amd64 debian/9.13 glibc/2.24 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.7
                UID:GID : 91994:4000
             netrc file : None
           offline mode : False


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    $ conda config --set report_errors true

rschwa@leander:/home/stud/rschwa$ echo $0
bash

Up to this point everything looked normal. The last line is because echo $0 is recommended when conda init fails.

The root of the issues might be the really old OS (Debian 9), something I cannot change right now. However, I could not find any info, that it is not supported anymore. Moreover, the error does not really look like something associated with too old OS. Anyway, I have no idea how to tackle it and would appreciate any help.

[milljm]

Almost looks like you might already have a Conda installation elsewhere?

Starting a new terminal with out having PATH=/home/stud/rschwa/miniforge:$PATH occurring, what happens when you invoke some conda commands? Namely, the following would be of interest:

conda info --all

If this returns command not found, well then I am wrong, and we need to focus elsewhere.

[milljm]

Sorry for the delayed response, it was our three day weekend.

export PATH=/home/stud/rschwa/miniforge/bin:$PATH
source activate /home/stud/rschwa/miniforge
conda info --all
conda list

You did exactly what I asked, and your print out is exactly what I expected (there shouldn't be any (moose) prompt). And it worked. So at least we have a work-around in the event we can't figure out conda init.

Next, lets do create the moose environment and see if we can activate that:

export PATH=/home/stud_syrinx/rschwa/miniforge/bin:$PATH
source activate /home/stud_syrinx/rschwa/miniforge
conda config --add channels https://conda.software.inl.gov/public
conda create -n moose moose-dev
source activate /home/stud_syrinx/rschwa/miniforge/envs/moose

If Conda successfully activate the moose environment, you should be able to build/run MOOSE. But I think the issue still remains "why doesn't conda init bash work". Does it now? After everything we've done?

conda init bash

[WulfHans]

rschwa@syrinx:~$ echo $PATH
/home/stud_syrinx/rschwa/miniforge/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/afs/tu-chemnitz.de/home/urz/r/rschwa/:/afs/tu-chemnitz.de/home/urz/r/rschwa/bin
rschwa@syrinx:~$ source activate /home/stud_syrinx/rschwa/miniforge/envs/moose
(moose) rschwa@syrinx:~$

Works fine, and compiling and using moose does work as well. So this works as workaround.

However, conda init bash still fails with exactly the same error as shown above (I will save the space for quoting it again).
Also, just conda init moose fails with the message Please call conda init first - but the command you gave me above using source activate works.

[milljm]

For your peace of mind, all of our build machines running the show here: https://civet.inl.gov, are using the same methods to activate the moose environment as you are at this point. Its a very clean way to do it. that is: it won't pick up anything stray from your bash/zsh/tcsh profiles by accident (and that is why we do it in our build environments).

Anyways! Not being able to run conda activate as a regular user is quite the inconvenience! Can we look at your bash (or whatever shell you are using) profiles? I think that would be the next logical step.

To prove if it is actually an environment profile issue getting in the way, does this work:

env -i bash --norc --noprofile
# some needed stuff
export HOME=/home/stud_syrinx
export PATH=/bin:/usr/bin:/sbin
export TERM=xterm-256color

# and now the troubleshooting:
export PATH=/home/stud_syrinx/rschwa/miniforge/bin:$PATH
conda init bash

Something I want to point out:

Also, just conda init moose

I am not sure this is a valid command to be honest. conda init <insert your terminal shell type here> is what should follow the init argument. Be it, ZSH, TCSH, BASH, etc type shells.

[WulfHans]

I solved it!

The bashrc template supplied by our central administration had some non-UTF8 symbols in a comment . German language has this wonderful thing called umlaut and some brilliant mind put them in the disclaimer and instruction comment block at the top (which I have not read carefully for years and have not bothered to copy here). It looks fine in any editor, but conda does not just append its block and is happy, it just dies to that.

Bottom line:

1. It was our own fault, but conda could be more error-tolerant or clear in its error messages.
2. I absolutely despise any encoding that is not utf-8
3. Thanks for your patience and support once more! I'll mark it as fixed.

[milljm]

We were certainly heading in the right direction! Cheers!