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Excerpt

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`

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titleTerminal 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


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:

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titleTerminal 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:

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