txrunn / jupyter-purcell

An innovative and collaborative solution for setting up and executing Jupyter Notebooks on High-Performance Computing (HPC) clusters, tailored for neuroscience data processing workflows.

Jupyter Starter

A set of scripts and configuration files to easily start Jupyter Notebooks on High-Performance Computing (HPC) servers. The repository can be found at github.com/txrunn/jupyter-purcell.

Quick Start

For a quick setup and to start the Jupyter Notebook on your chosen server, simply run:

MAKE SURE YOU ARE RUNNING BASH not TCSH

curl -O https://raw.githubusercontent.com/txrunn/jupyter-purcell/main/setup_and_run_jupyter.sh && \\
chmod +x setup_and_run_jupyter.sh && \\
chmod +x setup_and_run_jupyter.sh setup_environment.sh start.sh

./setup_and_run_jupyter.sh

This will download the necessary files, set up the Conda environment, and launch an interactive script to let you select a server and start Jupyter Notebook.

Detailed Setup

1. Clone the Repository:

   git clone https://github.com/txrunn/jupyter-purcell.git

2. Set Up the Conda Environment:

   • Navigate to the cloned repository directory:

     cd jupyter-purcell

   • Execute the setup_environment.sh script to set up the conda environment specified in the environment.yml file:

     ./setup_environment.sh

3. Configure Your Servers:

   • Edit the config.yaml file to specify your server details and desired port range.
   • To add more servers, simply extend the servers section in the config.yaml file.

Usage

1. Start Jupyter Notebook on HPC:
   • Run the open_jupyter.py script. If any dependencies are missing, you'll be prompted to install them:

     python open_jupyter.py

---

1. Clone the Repository:

   git clone https://github.com/txrunn/jupyter-purcell.git

2. Set Up the Conda Environment:

   • Navigate to the cloned repository directory:

     cd jupyter-purcell

   • Execute the setup_environment.sh script to set up the conda environment specified in the environment.yml file:

     ./setup_environment.sh

3. Configure Your Servers:

   • Edit the config.yaml file to specify your server details and desired port range.
   • To add more servers, simply extend the servers section in the config.yaml file.

Usage

1. Start Jupyter Notebook on HPC:

   • Run the open_jupyter.py script. If any dependency is missing, the script will notify you with instructions on how to install it:

     python open_jupyter.py

   • Follow the prompts to select your server and enter your username.
   • A web browser will open with your Jupyter Notebook session running on the HPC.

2. Terminate the Session:

   • When done with your Jupyter Notebook session, press Enter in the terminal where you started the session to terminate it.

Configuration

• The config.yaml file allows for customization of server details and port ranges.
• The environment.yml file specifies the Python environment and required packages for the Jupyter Notebook sessions.