Installing Miniconda on Ibex

Owned by Didier Barradas Bautista
Mar 21, 2023

Installing Miniconda

Login to Ibex using your KAUST credentials.

ssh $USERNAME@ilogin.ibex.kaust.edu.sa # use glogin.kaust.edu.sa if you need GPU nodes

Create a folder where you plan to install miniconda, which can be your home or scratch. In this example, we are going to use the home directory

mkdir ibex-miniconda-install/ cd ibex-miniconda-install/

Create a script (let's call it install-miniconda.sh) that allows you to install the latest version of miniconda, like this

# install miniconda in user's $HOME directory wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh rm Miniconda3-latest-Linux-x86_64.sh # source ~/.bashrc to load modifications source ~/.bashrc # update conda to most recent version (if necessary) conda update --name base --channel defaults --yes conda # install mamba (faster, experimental package manager) from Conda Forge conda install --name base --channel conda-forge mamba # make sure that base environment is not active by default conda config --set auto_activate_base false # second source required for update to conda config file to take effect source ~/.bashrc

Run the script by typing source install-miniconda.sh

The script will present several prompts that allow you to customize the Miniconda install. We generally
recommend that you accept the default settings. However, when prompted with the following...

Do you wish the installer to initialize Miniconda3 by running conda init?

...we recommend that you type no to avoid problems when you initialize Conda (reported by several users). Also, this is the same for Shaheen where you can not work with your environments if they are located at home (https://kaust-supercomputing-lab.atlassian.net/wiki/spaces/Doc/pages/516325377 )

You can also input each step on the command line one by one. Among these steps you see that we installed mamba , this is a parallel package installer (meaning your conda install runs faster)


To activate the base from the command line, type:

source $HOME/miniconda3/bin/activate


If you are still a little unsure about the whole process, we have created a tutorial on our
YouTube channel that will walk you through the above steps in detail.

 

http://www.youtube.com/watch?v=X-W7aVXH3_w

Uninstalling Miniconda

Login to Ibex using your KAUST credentials.

ssh $USERNAME@ilogin.ibex.kaust.edu.sa # use glogin.kaust.edu.sa if you need GPU nodes

Change into the ibex-miniconda-install directory and create a uninstall script. Sourcing
the script ensures that you don't need to log out of Ibex for the changes made by the uninstaller script to take effect.

cd ~/ibex-miniconda-install/

Create a bash script, and let's call it uninstall-miniconda.sh

# remove miniconda directory rm -rf ~/miniconda3 # remove the ~/.conda directory rm -rf ~/.conda # remove the ~/.condarc config file if necessary [ -f ~/.condarc ] && rm ~/.condarc # source ~/.bashrc to load modifications source ~/.bashrc

to run the script type :

source uninstall-miniconda.sh

You run this steps with the base environment is deactivated and there is no modification to the .bashrc file. again this is assuming you installed miniconda on your home directory

Running uninstall-miniconda.sh will delete all Conda environments stored in the
~/miniconda3/envs directory.