Migrating Environments

Migrating Environments#

Important

Many environments were created, by default, in user $WORK directories, which are deprecated as of January 15, 2025. Users with Conda environments they would like to keep using need to move or rebuild existing environments in a storage allocation created in ColdFront or their $HOME directory before August 15, 2025. Below are recommended ways to do this.

To see your existing environments, using the command mamba env list. Any projects that are in a subdirectory of /lustre/work/client/users/[YOUR USERNAME] will need to be moved or rebuilt if you are going to continue using them. We recommend always building your conda environment in the appropriate ColdFront storage allocation it is associated with. We do not recommend building environments in your $HOME directory because it is limited to 200GB of space.

Current Environments#

To get a list of dependencies and pip installed packages for an existing environment, run this command to save that list into an environment.yml file:

module load miniforge
mamba env export --no-builds -n mamba_env | grep -v "prefix" > environment.yml

Rebuild in a Storage Allocation#

To rebuild that environment in another directory:

mamba env create -f environment.yml -p /projects/[PI USERNAME]/[PROJECT DIRECTORY]/[STORAGE ALLOC DIRECTORY]/.conda/envs/mamba_env

Note

If this process does not work immediately, try removing versions numbers from packages within the environment.yml file before rebuilding it.

To use the new environment:

module purge
module load miniforge
mamba activate /projects/[PI USERNAME]/[PROJECT DIRECTORY]/[STORAGE ALLOC DIRECTORY]/.conda/envs/mamba_env

Rebuild in $HOME#

If you have not done so already, first make $HOME the default location for environments:

module load miniforge
conda config --set auto_activate_base false
conda config --prepend envs_dirs $HOME/.conda/envs
conda config --prepend pkgs_dirs $HOME/.conda/pkgs

To rebuild you environment in $HOME:

mamba env create -f environment.yml -p $HOME/.conda/envs/mamba_env

Note

If this process does not work immediately, try removing versions numbers from packages within the environment.yml file before rebuilding it.

To use the new environment:

module purge
module load miniforge
mamba activate -p $HOME/.conda/envs/mamba_env

Testing and Removing from $WORK#

Once you have tested your new environment to ensure it is working, please delete the environment from $WORK using:

mamba remove -p /lustre/work/client/users/[YOUR USERNAME]/.conda/envs/mamba_env/ --all