adios4dolfinx 0.8.0.dev0

Checkpointing functionality for DOLFINx meshes/functions with ADIOS2

ADIOS2Wrappers for DOLFINx

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This is an extension for DOLFINx to checkpoint meshes, meshtags and functions using ADIOS2.

The code uses the adios2 Python-wrappers to write DOLFINx objects to file, supporting N-to-M (recoverable) and N-to-N (snapshot) checkpointing. See: Checkpointing in DOLFINx - FEniCS 23 for more information.

For scalability, the code uses MPI Neighbourhood collectives for communication across processes.

Installation

Docker

ADIOS2 is installed in the official DOLFINx containers.

docker run -ti -v $(pwd):/root/shared -w /root/shared --name=dolfinx-checkpoint ghcr.io/fenics/dolfinx/dolfinx:nightly

Conda

To use with conda (DOLFINx release v0.7.0 works with v0.7.3 of ADIOS4DOLFINx)

conda create -n dolfinx-checkpoint python=3.10
conda activate dolfinx-checkpoint
conda install -c conda-forge fenics-dolfinx pip adios2
python3 -m pip install git+https://github.com/jorgensd/adios4dolfinx@v0.7.2

Functionality

DOLFINx

• Reading and writing meshes, using adios4dolfinx.read/write_mesh
• Reading and writing meshtags associated to meshes adios4dolfinx.read/write_meshtags
• Reading checkpoints for any element (serial and parallel, arbitrary number of functions and timesteps per file). Use adios4dolfinx.read/write_function.
• Writing standalone function checkpoints relating to "original meshes", i.e. meshes read from XDMFFile. Use adios4dolfinx.write_function_on_input_mesh for this.
• Store mesh partitioning and re-read the mesh with this information, avoiding calling SCOTCH, Kahip or Parmetis.

[!IMPORTANT]
For checkpoints written with write_function to be valid, you first have to store the mesh with write_mesh to the checkpoint file.

[!IMPORTANT]
A checkpoint file supports multiple functions and multiple time steps, as long as the functions are associated with the same mesh

[!IMPORTANT]
Only one mesh per file is allowed

Backwards compatibility

[!WARNING] If you are using v0.7.2, you are adviced to upgrade to v0.7.3, as it contains som crucial fixes for openmpi.

Legacy DOLFIN

Only checkpoints for Lagrange or DG functions are supported from legacy DOLFIN

• Reading meshes from the DOLFIN HDF5File-format
• Reading checkpoints from the DOLFIN HDF5File-format (one checkpoint per file only)
• Reading checkpoints from the DOLFIN XDMFFile-format (one checkpoint per file only, and only uses the .h5 file)

See the API for more information.

Long term plan

The long term plan is to get this library merged into DOLFINx (rewritten in C++ with appropriate Python-bindings).

Contributor guidelines

When contributing to this repository, please first create an issue containing information about the missing feature or the bug that you would like to fix. Here you can discuss the change you want to make with the maintainers of the repository.

Please note we have a code of conduct, please follow it in all your interactions with the project.

New contributor guide

To get an overview of the project, read the documentation. Here are some resources to help you get started with open source contributions:

• Finding ways to contribute to open source on GitHub
• Set up Git
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• Collaborating with pull requests

Pull Request Process

Pull Request

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• If you run into any merge issues, checkout this git tutorial to help you resolve merge conflicts and other issues.
• Please make sure that all tests are passing, github pages renders nicely, and code coverage are are not lower than before your contribution. You see the different github action workflows by clicking the "Action" tab in the GitHub repository.

Note that for a pull request to be accepted, it has to pass all the tests on CI, which includes:

• mypy: typechecking
• ruff: Code formatting
• pytest: Successfull execution of all tests in the tests folder.

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