Re: [petsc-users] Output data using ExodusIIViewer

Blaise Bourdin Wed, 01 Dec 2021 11:48:30 -0800

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 <[email protected]> wrote:

OK, let me have a look.
Blaise

On Nov 30, 2021, at 7:31 PM, David Andrs <[email protected]> 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 <[email protected]> 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 <[email protected]> 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

exo2.c
Description: exo2.c

Re: [petsc-users] Output data using ExodusIIViewer

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