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.
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:nightlyTo 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/[email protected]- 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.
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 v0.7.2, you are adviced to upgrade to v0.7.3, as it contains som crucial fixes for openmpi.
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
.h5file)
See the API for more information.
The long term plan is to get this library merged into DOLFINx (rewritten in C++ with appropriate Python-bindings).