6. Conda Environments

6.1. Obtaining Conda/Mamba

If conda and/or mamba is not available on a development machine, follow the instructions to download miniconda3 at Miniconda/Continuum Analytics website.

Note

It may be worth considering changing the default installation location to a partition with more space.

From the command line, enter:

df -h

to see how much space is available on the disk partitions on the host.

When asked to initialize Miniconda3 by running conda init, enter yes. This allows conda to append the user’s .bashrc file so that when the bash shell is invoked, the user will automatically be placed in a conda ‘base’ environment. This base environment is a very simple, minimal environment. From this base environment, the user can readily activate other conda envs.

6.2. Link Conda Directory to Data Disk (RAL Linux Machines)

By default, Conda environments are stored in a directory called “.conda” that is found in the user’s home directory, e.g. /home/user/.conda (Note that the dot at the beginning of the directory name is a hidden directory that does not always show up in a directory listing). Conda environments can take up a lot of disk space which can quickly fill up the /home disk. It is recommended that you create a directory on a data disk that has more disk space and create a symbolic link from the .conda directory so the environments will be stored on the data disk. Keep in mind that deleting the directory on the data disk will delete all of your conda environments and they cannot be easily recovered.

For all of the following commands, replace “user” with username.

1. Check if the .conda directory already exists.

   Run the following command:

   ls -al ~/ | grep .conda
   

   If nothing is output to the screen, then the directory does not exist and can proceed to step #3. If the screen output contains .conda followed by an arrow (->) followed by the path to a directory on a data disk, then the link has already been set up properly and no further action is needed. Example:

   .conda -> /d1/personal/user/conda
   

   If there is no arrow, then the contents of this directory need to be moved to the data disk.

2. Copy Existing Conda files to Data Disk.

   Determine the data disk location where personal files are stored. Examples:

   /d1/personal/user /d1/user

   Create a directory called conda in data directory. The name of this directory can be something else if desired. Modify the following commands as needed. Example:

   mkdir -p /d1/personal/$USER/conda
   

   Copy the contents of .conda in the home directory to this new directory:

   cp -r ~/.conda/* /d1/personal/$USER/conda/
   

   Now remove .conda from the home directory:

   rmdir ~/.conda
   

3. Create a symbolic link from .conda in the home directory to the directory that was just created.

   Example:

   ln -s /d1/personal/$USER/conda ~/.conda
   

4. Run the ls command again to confirm that there is now an arrow pointing to the new directory on the data disk.

   ls -al ~/ | grep .conda