Hdf5 and vtkhdf checkpoint

mattiafilips · November 9, 2026, 4:49pm

In io4dolfinx, there is the possibility to checkpoint a mesh with hdf5 backend. In dolfinx main repo, vtkhdf can also be used to write solution files, even if some work is still in progress (e.g. Improvements to VTKHDF format I/O · Issue #3582 · FEniCS/dolfinx · GitHub). Would it make sense to expose also some hdf5 compression options in the api? This could help in reducing the required storage for long time series or huge meshes.

Mattia

dokken · November 10, 2026, 1:40pm

Please add it to an issue in DOLFINx or IO4DOLFINx so I don’t forget it. I think it could be added with a patch to backend args:

src/io4dolfinx/backends/vtkhdf/backend.py

main


      
              dataset: h5py.Dataset, input_size: int, original_slice: tuple[int, int] | np.ndarray, mode: str
          ) -> slice:
              append_offset = dataset.shape[0] - input_size if mode == "a" else 0
              return slice(*(np.asarray(original_slice) + append_offset).astype(np.int64))
          
          
          def write_mesh(
              filename: Path | str,
              comm: MPI.Comm,
              mesh: MeshData,
              backend_args: dict[str, Any] | None,
              mode: FileMode,
              time: float,
          ):
              """
              Write a mesh to file.
          
              Args:
                  comm: MPI communicator used in storage
                  mesh: Internal data structure for the mesh data to save to file
                  filename: Path to file to write to

What specific compression options did you have in mind?

mattiafilips · November 10, 2026, 2:14pm

Ok, I opened the issue support hdf5 compression · Issue #96 · scientificcomputing/io4dolfinx · GitHub in io4dolfinx. I was thinking at classic gzip, but others could be interesting (HDF5: HDF5 Filters). For gzip compression, those options could be compression level and chunk size for example.

Mattia

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Hdf5 and vtkhdf checkpoint

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