[petsc-users] Output data using ExodusIIViewer

[Matthew Knepley]

Blaise, is that stuff we should be doing in the viewer?

  Thanks,

     Matt

On Wed, Dec 1, 2021 at 2:48 PM Blaise Bourdin <bourdin at mcmaster.ca> wrote:

> David,
>
> Here is a modified example.
> Exodus needs some additional work prior to saving fields. See the attached
> modified example.
>
> Blaise
>
>
> On Dec 1, 2021, at 1:54 PM, Blaise Bourdin <bourdin at mcmaster.ca> wrote:
>
> OK, let me have a look.
> Blaise
>
>
> On Nov 30, 2021, at 7:31 PM, David Andrs <andrsd at gmail.com> wrote:
>
> I see. I added a "Cell Sets" label like so:
> ​
> ​    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
>
> Blaise
>
> On Nov 30, 2021, at 9:50 AM, David Andrs <andrsd at gmail.com> wrote:
>
> Hello!
>
> 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
> MPI: MPICH 3.4.2
> Compiler: clang-12
>
> Call stack (not sure how relevant that is since it is from opt version):
>
> * 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);
>    460      ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);
>
> With regards,
>
> David Andrs
> <exo2.c>
>
>
> --
> 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
>
>
> --
> 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
>
>
> --
> 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
>
>

-- 
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/20211201/a6771352/attachment.html>