adios4dolfinx 0.4.0

Wrappers for reading/writing DOLFINx meshes/functions with ADIOS2

ADIOS2Wrappers for DOLFINx

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This is an experimental library for checkpoint with DOLFINx using ADIOS2.

Docker

ADIOS2 is installed in the official DOLFINx containers. To get access to the Python interface of ADIOS2 (inside dolfinx docker images), you might have to extend your Python-path:

docker run -ti -v $(pwd):/root/shared -w /root/shared --name=dolfinx-checkpoint ghcr.io/fenics/dolfinx/dolfinx:nightly
export PYTHONPATH=/usr/local/lib/python3/dist-packages:$PYTHONPATH

Conda

To use with conda (DOLFINx release v0.6.1 works with v0.1.0 of ADIOS4DOLFINx)

conda create -n dolfinx-checkpoint python=3.10
conda activate dolfinx-checkpoint
conda install -c conda-forge fenics-dolfinx pip adios2 numba
python3 -m pip install git+https://github.com/jorgensd/adios4dolfinx@v0.1.0

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

DOLFINx

• Reading and writing meshes, using adios4dolfinx.read/write_mesh
• Reading checkpoints for any element (serial and parallel, one checkpoint per file). Use adios4dolfinx.read/write_function.

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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