Nice-ODE Stack

Introduction

• This repository contains the instructions to build the containerized Nice-ODE stack from a linux machine
  • That is, linux desktop/cli -> linux container. Windows -> linux container is not supported at this time.
• Nice-ODE is a framework for optimizing the parameters of ODE's.
• Before building the stack you will need to install Docker.
  • For a local docker install I have found the Docker Desktop application has some sharp edges that can be avoided by installing the standalone Docker Engine (https://docs.docker.com/engine/install/), then managing the engine with VSCode's Docker extension (https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers).
  • Presumably you may also use Podman, but I have not tested it.

Components

• ./dockerfile
  • The central development container.
  • Installs dependencies needed to work with an 'advanced' Python setup
    • CUDA
    • Pytensor (PyMC dependency)
    • R integration
    • Poetry managed python dev-tools
• ./mlflow_image/
  • A local mlflow (https://mlflow.org/) server to track your work
  • Connects to a default PostgreSQL container defined in Nice-ODE's runtime docker compose file (not in this repo)
• ./gemma_llm/
  • Not constructed by default
  • A local Gemma 3 sever
  • You will need you own Hugging Face API key provisioned with read access to download the model weights.
  • Does not provide any additional functionality to the Nice-ODE stack.

Building

1. Clone this repo to your PC.

2. Open Terminal and cd into the directory where the repo was cloned

   1. eg. git_repos/nice-ode-stack

3. Run the bash script docker-compose-timestamp.sh as shown below.

   1. The compose log will be stored in ./docker_compose.log.
   2. If you run the command multiple times, consider updating the command to save the log to, for example, docker_compose2.log, docker_compose3.log etc.

• See the docker_compose.log_example if you want to check out what your log should look like.
• docker_compose.log_example is a text file and can be opened in any text editor.
• The file type is .log_example rather than .log because .log is ignored by git.

your-machine-name:~/git_repos/nice-ode-stack$ ./docker-compose-timestamp.sh > docker_compose.log 2>&1