Miniconda is a lean deployment of Python3, which is preferred here due to the reduced number of nodes it creates.

Install Miniconda3

1. Direct to home: cd ~

2. Download the latest version:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

3. Install to home directory:

bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3

4. Configure: conda init bash

Note: if the “conda command cannot be found”

  • run export PATH="/home/username/miniconda3/bin:$PATH" with “/home/username/miniconda3/” by “/your_home_directory/miniconda3”
  • to find you home directory: cd ~; pwd or click the “house” icon in WinSCP and look for the directory in “remote section”
  • run conda init bash again. Your screen may look like the picture below when Miniconda is activated

6. Optional: you can deactivate miniconda3 to save screen space and activate again before each use. If you skip this step, the miniconda3 will always be activated

    • Deactivate: conda config --set auto_activate_base false
    • Activate: conda activate
    • Deactivate again: conda deactivate

Install library for geometry clustering calculations:

1. Go back to home directory: cd ~

2. Check memory space: du -sh

  • any value below than 4.0 gb is fine
  • if not, run conda clean --all, choose y (yes) for all questions

3. Install pandas:pip install pandas

4. Install scikit-learn: pip install scikit-learn

5. Install matplotlib: pip install matplotlib

 

Optional: Deactivate Miniconda

you can deactivate miniconda3 to save screen space and activate again before each use. If you skip this step, the miniconda3 will always be activated

1. Deactivate: conda config --set auto_activate_base false

2. Activate: conda activate

3. Deactivate again: conda deactivate

 

Checking bashrc. file

The .bashrc file is a hidden script file which is executed when a user logs in. There are some commands that may need to be added manually to .bashrc file to make everything run without hiccups. Your .bashrc file should  look like the example below. Please check you .bashrc file in home directory and add commands if needed.

1. Directory home directory: cd ~

2. View the file: vi .bashrc

3. Modified as the picture above if need. All the “kimvu94” position will be change to you home folder name. To file you home folder name, follow the instructions above.

4. Save and quit: :wq! then hit <enter>