adios4dolfinx 0.7.2

Wrappers for reading/writing 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.

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 v0.7.1 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@v0.7.1

Long term plan

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

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Functionality

Implementation details

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.

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, one checkpoint per file). Use adios4dolfinx.read/write_function.

[!IMPORTANT]
For a checkpoint to be valid, you first have to store the mesh with write_mesh, then use write_function to append 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

[!WARNING] If you are using checkpoints written with adios4dolfinx prior to time-dependent/multi-function support, please use the legacy=True flag for reading in the checkpoint

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.

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