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conda

Move .conda Directory

Problem

The .conda directory might get quite beefy over time. This might cause problems with disk space (for example on the $HOME directory on an HPC cluster) and will need to be moved.

Solution

Move the .conda directory as usual:

mv $SOURCE/.conda $DESTINATION/.conda

Amend conda configuration:

conda config --remove pkgs_dirs $SOURCE/.conda/pkgs
conda config --add pkgs_dirs $DESTINATION/.conda/pkgs
conda config --remove envs_dirs $SOURCE/.conda/envs
conda config --add envs_dirs $DESTINATION/.conda/envs

Restart the shell. Everything should be good to go.

Using conda with SLURM

Problem

Many HPC clusters provide modules for Anaconda. However, the command conda activate ENV within a SLURM script fails with the following error:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.

The problem is that the (user-specific) .condarc configuration file is not being loaded when running a SLURM script with sbatch.

Solution

Use

#!/bin/bash -l

instead of #!/bin/bash at the top of the SLURM script.

The -l option forces bash to act as a login shell (thus loading the user-specific .condarc file) instead of acting as a blank shell.