<div dir="ltr">Blaise, is that stuff we should be doing in the viewer?<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 1, 2021 at 2:48 PM Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca">bourdin@mcmaster.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div style="overflow-wrap: break-word;">David,
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<div>Here is a modified example.</div>
<div>Exodus needs some additional work prior to saving fields. See the attached modified example.</div>
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<div>Blaise</div>
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<div>On Dec 1, 2021, at 1:54 PM, Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca" target="_blank">bourdin@mcmaster.ca</a>> wrote:</div>
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<div style="overflow-wrap: break-word;">OK, let me have a look.
<div>Blaise</div>
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<div>On Nov 30, 2021, at 7:31 PM, David Andrs <<a href="mailto:andrsd@gmail.com" target="_blank">andrsd@gmail.com</a>> wrote:</div>
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<div><font style="font-size:14px;font-family:sans-serif">
<div><font style="font-family:sans-serif;font-size:14px"><font style="font-size:14px"><font style="font-family:sans-serif">I see. I added a "Cell Sets" label like so:</font></font></font></div>
<div><font style="font-family:sans-serif;font-size:14px"><font style="font-size:14px"><font style="font-family:sans-serif"></font></font></font></div>
<div><font style="font-family:sans-serif;font-size:14px"><font style="font-family:monospace"><font style="font-size:14px"> DMCreateLabel(dm, "Cell Sets");</font></font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> DMLabel cs_label;</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> DMGetLabel(dm, "Cell Sets", &cs_label);</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> DMLabelAddStratum(cs_label, 0);</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> PetscInt idxs[] = { 1 };</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> IS is;</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> ISCreateGeneral(comm, 1, idxs, PETSC_COPY_VALUES, &is);</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> DMLabelSetStratumIS(cs_label, 0, is);</font></font></div>
<div><font style="font-family:monospace"><font style="font-size:14px"> ISDestroy(&is);</font></font></div>
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<div>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.</div>
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<div>This got me past the segfault, but now I see:</div>
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<div><font style="font-family:monospace">[0]PETSC ERROR: Argument out of range</font></div>
<div><font style="font-family:monospace">[0]PETSC ERROR: Number of vertices 1 in dimension 2 has no ExodusII type</font></div>
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<div>So, I assume I need to do something more to make it work.</div>
<div></div>
<div>David</div>
<div><font style="font-family:sans-serif"></font></div>
<div>On Nov 30 2021, at 11:39 AM, Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca" target="_blank">bourdin@mcmaster.ca</a>> wrote:</div>
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<div>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.</div>
<div>Can you see if that is enough? If not, I will go through your example</div>
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<div>Blaise</div>
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<div>On Nov 30, 2021, at 9:50 AM, David Andrs <<a href="mailto:andrsd@gmail.com" title="mailto:andrsd@gmail.com" target="_blank">andrsd@gmail.com</a>> wrote:</div>
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<div>Hello!</div>
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<div>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.</div>
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<div>Machine: MacBook Pro 2019</div>
<div>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</div>
<div>PETSc: Petsc Release Version 3.16.1, Nov 01, 2021</div>
<div>MPI: MPICH 3.4.2</div>
<div>Compiler: clang-12</div>
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<div>Call stack (not sure how relevant that is since it is from opt version):</div>
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<div><font style="font-family:monospace">* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0xc)</font></div>
<div><font style="font-family:monospace"> frame #0: 0x0000000102303ba9 libpetsc.3.16.dylib`DMView_PlexExodusII(dm=<unavailable>, viewer=<unavailable>) at plexexodusii.c:457:45 [opt]</font></div>
<div><font style="font-family:monospace"> 454 else if (degree == 2) nodes[cs] = nodesHexP2;</font></div>
<div><font style="font-family:monospace"> 455 }</font></div>
<div><font style="font-family:monospace"> 456 /* Compute the number of cells not in the connectivity table */</font></div>
<div><font style="font-family:monospace">-> 457 cellsNotInConnectivity -= nodes[cs][3]*csSize;</font></div>
<div><font style="font-family:monospace"> 458</font></div>
<div><font style="font-family:monospace"> 459 ierr = ISRestoreIndices(stratumIS, &cells);CHKERRQ(ierr);</font></div>
<div><font style="font-family:monospace"> 460 ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);</font></div>
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<div><font style="font-family:arial,sans-serif">With regards,</font></div>
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<div><font style="font-family:arial,sans-serif">David Andrs</font></div>
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<div><exo2.c></div>
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<div>Professor, Department of Mathematics & Statistics</div>
<div>Hamilton Hall room 409A, McMaster University</div>
<div>1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada </div>
<div>Tel. +1 (905) 525 9140 ext. 27243</div>
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<div>-- <br>
Professor, Department of Mathematics & Statistics<br>
Hamilton Hall room 409A, McMaster University<br>
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada <br>
Tel. +1 (905) 525 9140 ext. 27243</div>
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<div>-- <br>
Professor, Department of Mathematics & Statistics<br>
Hamilton Hall room 409A, McMaster University<br>
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada <br>
Tel. +1 (905) 525 9140 ext. 27243</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div>