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RUN_INSTRUCTIONS.md

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Running on a Server

This guide outlines the steps to set up and run PatientX on a server, including configuring a new installation directory, creating a virtual environment, and running the required scripts.

1. Creating a tmux Session (OPTIONAL but HIGHLY recommended)

Please reference tmux explanation documentation for more details on why to use tmux

To create a new session, run

tmux new -s session_name

2. SSH into HPC Cluster

SSH into the HPC platform where you would like to run the PatientX code

3. Creating a Virtual Environment in Python

Virtual environments are essential for managing dependencies and avoiding conflicts between different projects. This guide will walk you through creating and activating a virtual environment using venv.

Prerequisites

  • Make sure Python 3.10+ is installed on your system. You can check by running:

    python --version

    or

    python3 --version

Creating a Virtual Environment

Virtual environments can help us manage dependecies across projects and ensure there are no conflicting dependencies. To create a virtual environment, use the following command:

python -m venv {ENV_NAME}

This will create a new directory called myenv containing the virtual environment.

Activating the Virtual Environment

To activate the new virtual environment

On Windows

{ENV_NAME}\Scripts\Activate

On macOS and Linux

source {ENV_NAME}/bin/activate

4. Installing Dependencies

All dependecies and necessary packages for PatientX.AI can be installed by running

pip install -e .

5. Start Ollama Server (optional - for LLM representation model)

Install Ollama

Install ollama by either going through their documentation or, if you do not have sudo access, by running

./script/install.sh

Run Ollama Server

Run ollama server in the background by running

ollama serve &

Run LLM model

Run the chosen model using

ollama run model-name &

6. Run PatientX.AI Code

To run the PatientX.AI code

  1. Update the config file with your desired parameters
  2. Run the pipeline using
python src/PatientX/run.py
  1. For help, run
python src/PatientX/run.py --help

For further assistance, consult the PatientX documentation or contact the development team.