[petsc-users] HDF5 viewer + groups

[Matthew Knepley]

On Sun, May 10, 2020 at 10:03 PM Daniel R. Shapero <shapero at uw.edu> wrote:

> I'm trying to improve the checkpointing functionality in the Firedrake
> library, which currently uses the HDF5 viewer to store PetscVec objects.
> The problem with this approach is that a lot of context about the stored
> vector (e.g. the mesh and finite element space that it came from) is lost
> and we'd like to save that too.
>
> In order to make a sensible hierarchy inside the file, I'd like to be able
> to write a DMPlex to a group, say `/meshes/<mesh_name>`, within the file
> rather than at the root `/`. I tried using the `PETScViewerHDF5PushGroup`
> function; I thought that this will change the current group of the file to
> whatever name you give and all subsequent dataset writes will go under that
> group until you call the matching pop. This doesn't seem to be the case and
> all of the mesh data gets written under `/`. From reading the source code,
> it looks like the HDF5 writer pushes the group `/topology` to write out the
> DMPlex cells (and likewise for coordinates etc) which then clobbers
> whatever I pushed before it instead of concatenating.
>
> I've attached a minimal example using petsc4py to demonstrate. I get the
> same results when I use some extra functionality in Firedrake to ensure
> that the `/meshes` group is created in the first place, which I can then
> verify with h5ls.
>
> Is there a way to do what I want and if so how? If there isn't, is that
> because no one has needed this before or is there a fundamental reason why
> you shouldn't be doing this in the first place?
>

The reason is the impedence mismatch with visualization formats.
VTK/ExodusII/etc are all based on a single mesh and multiple vectors in a
file, so I
copied that design. It would be possible to namespace everything, and fix
the XDMF generator to understand that.

Vaclav, should we roll this into the HDF5 parallel reading/writing update?

  Thanks,

     Matt


> Thanks!
> Daniel
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200511/0387ef75/attachment.html>