DALIA

Python implementation of the methodology of integrated nested Laplace approximations (INLA), putting the accent on portability, modularity and performance (formerly known as PyINLA).

If you want to help us in the developement of DALIA, you can fill the following missing features survey: https://forms.gle/o4CxBDcr1t73pBHbA

If you want to get involved in the development of DALIA, please feel free to contact us directly.

Installation

DALIA is a python package that can be installed from its source code. You will need a working conda installation as well as the Serinv (https://github.com/vincent-maillou/serinv) solver library for accelerated solution of spatio-temporal models.

You can get a working installation of conda on the Miniconda website: https://repo.anaconda.com/miniconda/

This package relies on several libraries, some of which enabling high performance computing (HPC) features and GPU acceleration. These libraries (CuPy, MPI4Py, etc.) are not required for the basic functionality of the package, but are required for the advanced features.

Default required packages are:

conda install numpy scipy
conda install -c conda-forge pytest pytest-mpi pytest-cov coverage black isort ruff just pre-commit matplotlib tabulate numba -y

You can then optionally install the Serinv solver (required for spatio-temporal models)

cd /path/to/serinv/
python -m pip install -e .

And finally install the DALIA package:

cd /path/to/dalia/
python -m pip install -e .

We then recommend you to run some of the examples provided in the examples/ directory to test your installation. For more detailed installation instructions, especially on clusters, leveraging GPU acceleration through CuPy and distributed computing through MPI4Py, please refer to the dev note in the DEV_README.md file.

Examples

Some examples are provided with running scripts. The examples are being tracked using git-lfs, to download them, run the following commands:

git lfs pull
git lfs checkout

You can then navigate in the examples/ directory and run the given examples. For example, to run a Gaussian Spatio-Temporal model, you can run:

python gst_small/run.py

Known Installation Issues

The sqlite module might not work properly. Forcing the following version of sqlite might help:

conda install conda-forge::sqlite=3.45.3