Conda set LD_LIBRARY_PATH for env only [duplicate]

Question

I have an installation of miniconda3 where I have created a virtual environment called py35. I have some libraries that I only want to use from within this environment. hence they are under

 /.../miniconda3/envs/py35/libs

However they are not found from within the environment as LD_LIBRARY_PATH does not contain said folder. I now want to set LD_LIBRARY_PATH to include the /lib only when I am in the virtual environment.

I was thinking of modifying the activate script miniconda uses to start the environment but am not quite sure if this is standard practice or if there is an easier way to achieve this.

Fascine

Answer 1

You can set environment variables when an environment is activated by editing the activate.d/env_vars.sh script. See here: https://conda.io/docs/user-guide/tasks/manage-environments.html#macos-and-linux

The key portions from that link are:

1. Locate the directory for the conda environment in your Terminal window, such as /home/jsmith/anaconda3/envs/analytics.

2. Enter that directory and create these subdirectories and files:

   cd /home/jsmith/anaconda3/envs/analytics
   mkdir -p ./etc/conda/activate.d
   mkdir -p ./etc/conda/deactivate.d
   touch ./etc/conda/activate.d/env_vars.sh
   touch ./etc/conda/deactivate.d/env_vars.sh
   

3. Edit ./etc/conda/activate.d/env_vars.sh as follows:

   #!/bin/sh
   
   export MY_KEY='secret-key-value'
   export MY_FILE=/path/to/my/file/
   

4. Edit ./etc/conda/deactivate.d/env_vars.sh as follows::

   #!/bin/sh
   
   unset MY_KEY
   unset MY_FILE
   

When you run conda activate analytics, the environment variables MY_KEY and MY_FILE are set to the values you wrote into the file. When you run conda deactivate, those variables are erased.

Epizootic

Exactly what I was looking for. Thank you. Only small alteration since I add something to LD_LIBRARY_PATH I cannot use unset. Instead I do export LD_LIBRARY_PATH=${LD_LIBRARY_PATH/'PATH_I_ADDED/""}` in the deactivation script – Fascine

Upvoted, useful stuff. Is there a way of doing this when creating the environment? does not seem the right thing to do with automated deployment – Ferrick

@Ferrick There are pre-link, post-link, and post-unlink scripts that are used when a package is installed, which occurs on environment creation. – Epizootic

Is there a good reason why this is not done automatically by conda? After all, the user of an environment is expected to be able to use mutually-dependent libraries by activating the environment. A lot of these environment-specific packages are shared libraries and python wrappers for them, so when would you NOT want to do this? Shouldn't env-specific .so files ALWAYS take precedence over other locations? – Cilo

This works well, but should be combined with @Oleksandr answer here. However, it does not seem to have an effect on Jupyter notebooks :-( – Orthopteran

Answer 2

I just wanted to add that you could declare 2 variables in the activate.d/env_vars.sh like, it makes it easier to reset the variable to the pre-activation state:

export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=/your/path:${LD_LIBRARY_PATH}

and then in deactivate.d/env_vars.sh:

export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}
unset OLD_LD_LIBRARY_PATH

Rossman

Highly recommend this if you need to keep the original values around. Been using this solution and works well. – Zettazeugma

Awesome, worked well! – Alderson

Just remember that if you have your env activated and you deactivate it firstly after having modified the files, this will erase your LD_LIBRARY_PATH variable. It just happened to me, I hope it won't happen to someone else. – Flaxman

Also use export LD_LIBRARY_PATH=/your/path:${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} in case your library path was empty. – Armes