[petsc-dev] Plex XDMF/HDF5 I/O

[Vaclav Hapla]

For DMPlex and PETSCVIEWERHDF5, DMView produces a HDF5 file consisting basically of these 3 parts:
1) vertices (HDF5 group /geometry)
2) "native" Plex topology as a serialization of the Plex graph
3) traditional topology as connectivity of vertices, XDMF-compatible (HDF5 group /viz/topology)
So the topology is stored redundantly in two different ways 2 and 3.

I'm now a member of the team developing the Salvus application, and we would like to use XDMF-compatible HDF5 as our native format. I would be glad if PETSc took care of this completely instead of coding it just for Salvus.

Looking how it is now in PETSc, I'm tempted to implement a new separate Viewer for reading and writing purely this HDF5 flavor, i.e. parts 1 and 3. It also looks to me easier for parallel I/O and support by external tools like https://github.com/nschloe/meshio. The writer code can be copy-pasted from plexhdf5.c (function DMPlexWriteTopology_Vertices_HDF5_Static) and the reader can be implemented relatively easily using DMPlexCreateFromCellListParallel (see preview at https://bitbucket.org/haplav/petsc/commits/4719ef6a33f5f9a4a1b8c81c7a6e6ed0426097f1?at=haplav/feature-dmplex-distributed-hdf5-read).

It would of course not support any possible DMPlex instance, but what is supported by XDMF forms a sensible subset for practical use. The current HDF5 could be kept as a native PETSc format allowing storing any possible DMPlex. But I would then remove part 3 from this format, getting rid of "Visualization topology currently only supports..." errors currently thrown by DMView.

There's still a question how to store non-homogenous meshes (with different cell shapes). I can see two possible ways:
1) Store separate "sections" of a mesh, each section with homogenous cell shape. Matt: "This might mean that you need to permute the numbering to group cells of the same shape, which is already making me feel tired."
2) XDMF allows "mixed" topology (http://www.xdmf.org/index.php/XDMF_Model_and_Format#Arbitrary) where cell shape is specified per cell. The problem is that each row representing a cell would have different number of values. This is not nice for current ISView/VecView with fixed block size.
It will also require generalising DMPlexCreateFromCellListParallel().

Later on I would consider generating the XDMF XML file directly by this Viewer without having to call the python script $PETSC_DIR/bin/petsc_gen_xdmf.py afterwards.

Any comments on this?

Thanks

Vaclav