[petsc-dev] getting ready for PETSc release

[Blaise A Bourdin]

Resending to the list:


I saw that. Does it mean that all heavy data is duplicated in the hdf5 file, i.e. that /fields contains values that petsc understands and /viz is for visualization?

Yes, this is controlled by the viewer format. I saw no way to get xmf to look at scattered data, so duplication was inevitable.

There are two issues:
projection into linear / bilinear elements that xdmf understands and scattered data.
I think that one way to deal with the later is to create one grid per cell set. the hierarchy should be
    <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
      <Time TimeType="HyperSlab”>
:
:
      </Time>
      <Grid Name="Mesh" GridType="Collection" CollectionType="Spatial">
<Grid Name="cellset000001" GridType="Uniform">
:
:
</Grid>
<Grid Name="cellset000002" GridType="Uniform">
:
:
</Grid>
    </Grid>
i.e. one connectivity table per cell set instead of a global one. This also addresses the issue of different element types
Lastly, when no interpolation is needed, we do not need to duplicate results in the hdf5 file this way.

How hard would it be to split the connectivity table in the hdf5 file? Once this is done, I can try to write a xmd file by hand for reference.

The xmf generation script fails on it, most likely because I don’t have a /time section in the file. My workaround is to replace l. 209 with time = [0,1].

The xmf script works on it now.

Did you push your changes? I have switched to next but still get an error:
bourdin at galerkin:DMComplex $ $PETSC_DIR/bin/pythonscripts/petsc_gen_xdmf.py TwoSquares.h5
Traceback (most recent call last):
  File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 220, in <module>
    generateXdmf(sys.argv[1])
  File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 215, in generateXdmf
    Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields, cfields)
  File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 176, in write
    self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim)
  File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 75, in writeSpaceGridHeader
    ''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if spaceDim > 2 else "XY"))
KeyError: 1

I need to understand how xmf treats these mixes meshes. This is where help would be useful.
The checkpointing works with them however.

I struggled with the same problem until Jinghua Ge, our viz expert and xmf / hdf5 guru, suggested to use a spatial collection of spatial grids.

Blaise
--
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin
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