How to create a python environment for you cluster jobs

Create a new python environment and make sure obob_condor gets installed in it

Open a terminal and navigate to your folder on /mnt/obob:

cd /mnt/obob/staff/thartmann

Now create a new folder where you want to store the code and the environment:

mkdir my_obob_condor_test
cd my_obob_condor_test

Create a file called environment.yml. This file lists all the conda and pypi packages your project needs. Take a look here for a description. For this tutorial, it should look like this:

channels:
  - defaults
  - conda-forge

dependencies:
  - pip
  - spyder
  - pip:
      - obob_condor

You can use any text editor you like, but if you are connected via X2go or remote desktop, the easiest way is to start a nice graphical text editor like this:

gedit environment.yml

If you wanted to analyze actual data with it, you would probably need to add mne, pandas, etc. to it. But we can leave it like this.

Copy-paste the content in there, save and exit and go back to the terminal.

You can now create the environment like this:

mamba env create -p ./.venv

When this is done, you must activate the environment:

conda activate ./.venv

And then start Spyder (a Python editor) like this:

spyder

Before you go on, make sure that:

  1. The folder that is shown in the box on the top right, just below the menu bar is the folder you just created. If not, click the folder button to the right and navigate to the correct one.

  2. Just below, you find a pane which has four different tab options: “Help”, “Variable Explorer”, “Plots” and “Files”. Make sure “File” is selected.

You should now see the environment.yml file that we created before.