Dear Matt,

    I guess you're right: thresholding by rank==0 and rank==1 in paraview reveals that it is indeed the overlap cells that are appear twice in the output.

The attached file is not exactly minimal but hopefully short enough. If I run it in serial, all is ok, but with

    mpirun -np 2 ./saveDemo

it creates a 10x10 grid, but I get "output.vtu" with a total of 120 cells. However the pointSF of the DMPlex seems correct.

Thanks

    Matteo

On Mon, Oct 21, 2024 at 12:22 PM Matteo Semplice via petsc-users <petsc-users@mcs.anl.gov> wrote:

Dear petsc-users,

    I am having issues with output of parallel data attached to a DMPlex (or maybe more fundamental ones about DMPlex...).

So I currently

1. create a DMPlex (DMPlexCreateGmshFromFile or DMPlexCreateBoxMesh)
2. partition it
3. and create a section for my data layout with DMPlexCreateSection(ctx.dmMesh, NULL, numComp, numDof, numBC, NULL, NULL, NULL, NULL, &sUavg)
4. DMSetLocalSection(ctx.dmMesh, sUavg)
5. create solLoc and solGlob vectors with DMCreateGlobalVector and DMCreateLocalVector
6. solve ....
7. VecView(ctx.solGlob, vtkViewer) on a .vtu file
   

but when I load data in ParaView I get more cells than expected and it is as if the cells in the halo are put twice in output. (I could create a MWE if the above is not clear)

I think we need an MWE here, because from the explanation above, it should work.

However, I can try to guess the problem. When you partition the mesh, I am guessing that you have cells in the overlap. These cells

must be in the point SF in order for the global section to give them a unique owner. Perhaps something has gone wrong here.

  Thanks,

     Matt 

I guess that the culprit is point (4), but if I replace it with DMSetGlobalSection then I cannot create the local vector at point (5).

How should I handle this properly? In my code I need to create both local and global vectors, to perform at least GlobalToLocal and to save the global data.

(On a side note, I tried also HDF5 but then it complains about the DM not having a DS...; really, any working solution that allows data to be explored with Paraview is fine)

Thanks for any advice!

Matteo Semplice

--

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/

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Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como