[petsc-users] Output data using ExodusIIViewer

[David Andrs]

I see. I added a "Cell Sets" label like so:
  
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​        DMCreateLabel(dm, "Cell Sets");
  
       DMLabel cs_label;
  
       DMGetLabel(dm, "Cell Sets",  &cs_label);
  
       DMLabelAddStratum(cs_label, 0);
  
       PetscInt idxs[] = { 1 };
  
       IS is;
  
       ISCreateGeneral(comm, 1, idxs, PETSC_COPY_VALUES,  &is);
  
       DMLabelSetStratumIS(cs_label, 0, is);
  
       ISDestroy(&is);
  
  
Note, that I have only a single element (Quad4) in the mesh and I am just trying to get this working, so I understand what needs to happen for larger meshes.
  
​
  
​This got me past the segfault, but now I see:
  
​
  
[​0]PETSC ERROR: Argument out of range
  
[0]PETSC ERROR: Number of vertices 1 in dimension 2 has no ExodusII type
  
  
So, I assume I need to do something ​more to make it work.
  
​
  
​David
  
​​
  
On Nov 30 2021, at 11:39 AM, Blaise Bourdin  <bourdin at mcmaster.ca>  wrote:
  
>   
> It looks like your DM cannot be saved in exodus format as such. The exodus format requires that all cells be part of a single block (defined by ‘Cell Set’ labels), and that the cell sets consists of sequentially numbered cells.
>   
> Can you see if that is enough? If not, I will go through your example
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> Blaise
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> >   
> > On Nov 30, 2021, at 9:50 AM, David Andrs  <andrsd at gmail.com (mailto:andrsd at gmail.com)>  wrote:
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> > Hello!
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> >
> >   
> > I am trying to store data into an ExodusII file using the ExodusIIViewer, but running into a segfault inside PETSc. Attached is a minimal example showing the problem. It can very much be that I am missing something obvious. However, if I change the code to VTKViewer I get the desired output file.
> >   
> >
> >   
> > Machine: MacBook Pro 2019
> >   
> > OS version/type:   Darwin notak.local 21.1.0 Darwin Kernel Version 21.1.0: Wed Oct 13 17:33:23 PDT 2021; root:xnu-8019.41.5~1/RELEASE_X86_64 x86_64
> >   
> > PETSc:   Petsc Release Version 3.16.1, Nov 01, 2021
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> > MPI: MPICH 3.4.2
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> > Compiler: clang-12
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> >
> >   
> > Call stack (not sure how relevant that is since it is from opt version):
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> >
> >   
> > * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0xc)
> >   
> >        frame #0: 0x0000000102303ba9 libpetsc.3.16.dylib`DMView_PlexExodusII(dm=<unavailable>, viewer=<unavailable>) at plexexodusii.c:457:45 [opt]
> >   
> >       454                else if (degree == 2) nodes[cs] = nodesHexP2;
> >   
> >       455            }
> >   
> >       456            /* Compute the number of cells not in the connectivity table */
> >   
> > ->  457            cellsNotInConnectivity -= nodes[cs][3]*csSize;
> >   
> >       458
> >   
> >       459            ierr = ISRestoreIndices(stratumIS,  &cells);CHKERRQ(ierr);
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> >       460            ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);
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> >   
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> >   
> > With regards,
> >   
> >   
> >
> >   
> > David Andrs
> >   
> >   
> > <exo2.c>
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> --   
>   
> Professor, Department of Mathematics  &   Statistics
>   
> Hamilton Hall room 409A, McMaster   University
>   
> 1280 Main Street West, Hamilton,   Ontario L8S 4K1, Canada   
>   
> Tel. +1 (905) 525 9140 ext. 27243
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