Thursday, 4 May 2023

conda can't find platform independent libraries

I am having issues with conda. I am working on a cluster (red hat linux), and I successfully managed to use conda, create an environment called envname (containing python2.7) and installing some modules. One day I logged in and I got this error when trying to launch conda (either conda activate envname or some simple command like conda info):

Could not find platform independent libraries <prefix>

Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]

Python path configuration:

PYTHONHOME = (not set)

PYTHONPATH = (not set)

program name = '/path/to/anaconda3/bin/python'

isolated = 0

environment = 1

user site = 1

import site = 1

sys._base_executable = '/path/to/anaconda3/bin/python'

sys.base_prefix = '/tmp/build/80754af9/python_1593706424329/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho'

sys.base_exec_prefix = '/path/to/anaconda3'

sys.executable = '/path/to/anaconda3/bin/python'

sys.prefix = '/tmp/build/80754af9/python_1593706424329/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho'

sys.exec_prefix = '/path/to/anaconda3'

sys.path = [ '/tmp/build/80754af9/python_1593706424329/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python38.zip', '/tmp/build/80754af9/python_1593706424329/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8', '/path/to/anaconda3/lib/python3.8/lib-dynload', ]

Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding

Python runtime state: core initialized

ModuleNotFoundError: No module named 'encodings'

Current thread 0x00007fbecd9dd740 (most recent call first): <no Python frame>

My goal is to make conda run again with the virtual environment I previously created, without having to install everything from scratch.

I tried to look up similar threads but could not solve the problem. Some possibly relevant informations:

  1. By doing source activate envname (what I usually did ti activate the virtual environment) it gives the error -bash: activate: File o directory non esistente

  2. If I use the python command right after logging in the cluster, I have a function python (version 2.7). As expected, it does not have installed all the modules I have installed on the conda environment.

  3. By using the command which python, I can see that this python version is located in /usr/bin/python. This folder is not my personal folder on the cluster, rather a global one. So I guess exploring the solution proposed here (Could not find platform independent libraries <prefix>) can't be applied due to permission (although I have not tried it)

  4. If I try to manually set the PYTHONHOME variable by using export PYTHONHOME=/usr/bin/python, not only conda does not work, but also the python command does not work, giving the error "could not import site"

  5. The same is still true if I try to set to the same path also the PYTHONPATH and PATH variables, in addition to the PYTHONHOME variable.

  6. If I unset the PYTHONHOME and other paths, or log out of the cluster and then log in again, python works as described in the first bullet point.

  7. Same is true if instead of /usr/bin/python I use the /path/to/anaconda3/bin/python for PYTHONHOME, PYTHONPATH and PATH (it only changes the error message displaying the updated paths)

  8. In PATH there are the following paths: '/path/to/anaconda3/condabin', '/usr/bin' (among other paths). If I append to .bashrc the line export PATH=$PATH:/path/to/anaconda3/bin and source again the .bashrc file, the problem persists. (this solution was suggested here Can't find my conda environment)



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