How to Configure Conda to Avoid Quota Issues

Conda is a popular package manager. However, Conda creates many small files when installing packages, which can quickly fill your quota on /software. This article will tell you how to configure Conda to avoid this issue. Please note that these instructions also work for Mamba, which is a much faster drop-in replacement for Conda.

Installation

When you install Conda, it is best practice to install in your software partition, i.e. $MYSOFTWARE or `/software/projects/$PAWSEY_PROJECT/$USER/miniconda3`

Configuration

When Conda installs packages, it writes a lot of small files, which can quickly fill up your quota on /software. To avoid this issue, you can configure Conda via the .condarc file to put all those package files into the /scratch partition instead. There are two ways to update your .condarc file. The first way allows you to update your .condarc file from the command line. Ensure you edit the command below to match your project ID and user name:

Terminal 1. Installing miniconda

$ mkdir -p $MYSOFTWARE/miniconda3
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $MYSOFTWARE/miniconda3/miniconda.sh
$ bash $MYSOFTWARE/miniconda3/miniconda.sh -b -u -p $MYSOFTWARE/miniconda3
$ rm -rf $MYSOFTWARE/miniconda3/miniconda.sh

Note - If you get a Disk Quota exceeded error, your home dir might be filled up so try cleaning by removing the dir and then creating it in the software and generating a symbolic link.

Terminal 2. Conda configuration editing on command line

$ conda config --add pkgs_dirs /scratch/pawsey0000/user_name/conda_cache

The second option is to open the .condarc file in a text editor and add the following lines, edited to match your project code and user name:

Terminal 3. Example update of ~/.condarc file

pkgs_dirs:
- /scratch/pawsey0000/user_name/conda_cache

Cleaning up

Conda supports users cleaning up old package files you no longer need. It’s important to do this regularly to avoid overburdening the Lustre filesystem on /scratch. To clean up, simply run:

Terminal 4. Cleaning up unneeded cache files

$ conda clean -af