[petsc-users] Output data using ExodusIIViewer
David Andrs
andrsd at gmail.com
Thu Dec 2 09:02:22 CST 2021
Blaise,
thank you very much for you help. This helps a lot.
By the way, I was not able to open the produced file in paraview 5.9.1 (failed with "EX_INQ_TIME failed"). However, ncdump seems correct. At least, I do not immediately see anything wrong there. I will try to look into this problem myself, now that I know it is ok to do direct exodusII calls.
Thank you again,
David
On Dec 1 2021, at 12:48 PM, Blaise Bourdin <bourdin at mcmaster.ca> wrote:
>
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> David,
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> Here is a modified example.
>
> Exodus needs some additional work prior to saving fields. See the attached modified example.
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> Blaise
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> > On Dec 1, 2021, at 1:54 PM, Blaise Bourdin <bourdin at mcmaster.ca (mailto: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 (mailto: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 (mailto: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 (mailto: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>
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> > > >
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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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> > --
> >
> > 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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> --
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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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