Repository for the AdoptODE Package introduced in "Tutorial: a beginner’s guide to building a representative model of dynamical systems using the adjoint method" (https://doi.org/10.1038/s42005-024-01606-9).
This repository contains the adoptODE code as well as example notebooks for setting up systems similar to those in the publication.
Documentation is also provided here: https://sherzog3.pages.gwdg.de/adoptODE/
AdoptODE relies on JAX, for an installation of adoptODE a functioning JAX installation needs to be ensured. To use adoptODE and JAX with GPU support, which we recommend at this point, you must first install CUDA and CuDNN. If you already have a working JAX installation, you can add adoptODE to your active environment by running
user@workstation:~/adoptode pip install .in the repository directory.
If this is ensured, adoptODE including JAX can be installed comparatively easily in a conda environment, e.g:
user@workstation:~/adoptode conda create --name adoptODE python=3.12
user@workstation:~/adoptode conda activate adoptODE
user@workstation:~/adoptode pip install --upgrade pip
user@workstation:~/adoptode pip install -r requirements_gpu.txtuser@workstation:~/adoptode conda create --name adoptODE python=3.12
user@workstation:~/adoptode conda activate adoptODE
user@workstation:~/adoptode pip install --upgrade pip
user@workstation:~/adoptode pip install -r requirements_cpu.txtAs an alternative to local installations or conda environments, you can also use the container file for apptainer or singularity , providing a minimal environment for adoptODE.
For a container with GPU support run:
user@workstation:~/adoptode/container apptainer build adoptODE_GPU.sif adoptODE_GPU.defAfter that, you can do a shell run in the container:
user@workstation:~/adoptode/container apptainer shell --nv adoptODE_GPU.sifTo set up the container file run:
user@workstation:~/adoptode/container apptainer build adoptODE_CPU.sif adoptODE_CPU.defAfter that, you can do a shell run in the container:
user@workstation:~/adoptode/container apptainer shell adoptODE_CPU.sif├── LICENSE
├── README.md <- Git markdown file
├── data
│ ├── SolarSystem <- Data to reproduce the Gravitational N-body systems (Solar System) system case from the paper.
│ └── Zebrafish <- Subset of the zebrafish data.
│
├── container <- Folder with container defintions for apptainer/singularity
│ ├── adoptODE_GPU.def
│ └── adoptODE_CPU.def
│
├── notebooks <- Jupyter notebooks with exemplary implementations as they appear in the paper. Note: In some cases, the dimensions of the systems are smaller than the published values.
│ ├── BOCF.ipynb
│ ├── LotkaVolterra.ipynb
│ ├── RayleighBenard.ipynb
│ ├── RepulsiveSpheres.ipynb
│ ├── SolarSystem.ipynb
│ └── Zebrafish.ipynb
│
├── adoptODE <- Sorce code folder
│ ├── Framework.py <- Framework defintion of adoptODE
│ ├── ODE_Exp_dt.py <- Adaption of the JAX included ODE solver
│ ├── ODE_Fix_dt.py <- Adaption of the JAX included ODE solver
│ └── OptBounded.py <- Customisation of some of the included optimisers in JAX
│
├── requirements_gpu.txt <- The requirements file to install adoptODE with GPU support
├── requirements_cpu.txt <- The requirements file install adoptODE without GPU support
└── setup.py <- makes project pip installable (pip install -e .) so adoptODE can be imported
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