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Scalable GIS for Urbanists: Setup

Before the workshop

  • Windows users are strongly recommended to install Windows Subsystem for Linux 2 (WSL). For instructions, see Windows section below.
  • Participants should have Python 3 and SSH. In order to verify whether these are installed and/or to install them on MacOS, Linux, or Windows, see the Appendix section below.
  • Two Python packages are required: Fabric and Decorator. To install them, type in a terminal window: 
    pip install fabric decorator
    (Participants familiar with conda or venv, can create an environment with the following dependencies: python=3.10, fabric, decorator)
  • Download and extract the following zip archive: link
  • Test the setup:
    • Access the extracted folder in your terminal (you might have to modify the path below): 
      cd ~/Downloads/JupyterDaskOnSLURM-workshops
    • Running: 
      python runJupyterDaskOnSLURM.py
      should return: 
      usage: runJupyterDaskOnSLURM.py [-h] [--local_port LOCAL_PORT] [--wait_time WAIT_TIME] (--add_platform | --one_off | --uid UID) [--mode MODE]
runJupyterDaskOnSLURM.py: error: one of the arguments --add_platform/-a --one_off/-oo --uid/-u is required

On the day of the workshop

  • Download the SSH key for Spider using the link on the printout.
  • Access the JupyterDaskOnSLURM-workshops folder in your terminal (you might have to modify the path below): 
    cd ~/Downloads/JupyterDaskOnSLURM-workshops
  • Edit the configuration file config/platforms/platforms.ini with your account information:
    • You can use nano (e.g. nano config/platforms/platforms.ini to start editing, Ctrl+X to quit);
    • Replace the user name stursdat-XX with your user ID (e.g. stursdat-01);
    • Replace the SSH key path /path/to/the/ssh-key/rsa_stursdat_XX with the actual file path (e.g. /Users/fnattino/Downloads/rsa_stursdat_01).
  • Start a Jupyter session on Spider by running the following command: 
    python runJupyterDaskOnSLURM.py --uid spider-stursdat --mode run
    Jupyter Lab should open up in your browser!

Appendix: System specific instructions

MacOS:

  • To install any of the tools below, you can use Homebrew or an alternative package manager.
  • Python
    • You can test whether Python is installed by opening Terminal and by typing: 
      python3 --version
      which should output ‘Python 3.X.Y’
    • If above fails, install Python 3 (we recommend python 3.10): 
      brew install python@3.10
  1. SSH
    • You can test whether SSH is installed by opening Terminal and by typing: 
      ssh
      which should output a list of usage options.
    • If above fails, install SSH: 
      brew install openssh

Linux:

  • Python
    • You can test whether Python is installed by opening Terminal and by typing: 
      python3 --version
      which should output ‘Python 3.X.Y’
    • If above fails, install Python 3 (we recommend python 3.10) using the distribution package manager. For Ubuntu: 
      sudo apt-get install python3.10
  1. SSH
    • You can test whether SSH is installed by opening Terminal and by typing: 
      ssh
      which should output a list of usage options.
    • If above fails, install SSH using the distribution package manager. For Ubuntu: 
      sudo apt install openssh-server

Windows:

  1. Windows subsystem for linux 2 (WSL); To install WSL:
    • Open PowerShell as administrator
    • Run wsl --install (by default the Ubuntu distribution will be installed)
    • Restart PC
    • After restarting, follow the instructions on the automatically opened Ubuntu terminal to setup ubuntu ID and password
    • From now on, follow the above instructions as given for Linux, using the Ubuntu terminal to type in commands.