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OK, let me have a look.
<div class="">Blaise</div>
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<div class="">On Nov 30, 2021, at 7:31 PM, David Andrs <<a href="mailto:andrsd@gmail.com" class="">andrsd@gmail.com</a>> wrote:</div>
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<div class=""><font style="font-family:sans-serif;font-size:14px" class=""><font style="font-size:14px" class=""><font style="font-family:sans-serif" class="">I see. I added a "Cell Sets" label like so:</font></font></font></div>
<div class=""><font style="font-family:sans-serif;font-size:14px" class=""><font style="font-size:14px" class=""><font style="font-family:sans-serif" class=""></font></font></font></div>
<div class=""><font style="font-family:sans-serif;font-size:14px" class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> DMCreateLabel(dm, "Cell Sets");</font></font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> DMLabel cs_label;</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> DMGetLabel(dm, "Cell Sets", &cs_label);</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> DMLabelAddStratum(cs_label, 0);</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> PetscInt idxs[] = { 1 };</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> IS is;</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> ISCreateGeneral(comm, 1, idxs, PETSC_COPY_VALUES, &is);</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> DMLabelSetStratumIS(cs_label, 0, is);</font></font></div>
<div class=""><font style="font-family:monospace" class=""><font style="font-size:14px" class=""> ISDestroy(&is);</font></font></div>
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<div class="">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 class="">This got me past the segfault, but now I see:</div>
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<div class=""><font style="font-family:monospace" class="">[0]PETSC ERROR: Argument out of range</font></div>
<div class="p1"><font style="font-family:monospace" class="">[0]PETSC ERROR: Number of vertices 1 in dimension 2 has no ExodusII type</font></div>
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<div class="p1">So, I assume I need to do something more to make it work.</div>
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<div class="p1">David</div>
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<div class="gmail_quote_attribution">On Nov 30 2021, at 11:39 AM, Blaise Bourdin <<a href="mailto:bourdin@mcmaster.ca" class="">bourdin@mcmaster.ca</a>> wrote:</div>
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<div class="">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 class="">Can you see if that is enough? If not, I will go through your example</div>
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<div class="">Blaise</div>
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<div class="">On Nov 30, 2021, at 9:50 AM, David Andrs <<a href="mailto:andrsd@gmail.com" title="mailto:andrsd@gmail.com" class="">andrsd@gmail.com</a>> wrote:</div>
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<div class="">Hello!</div>
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<div class="">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 class="">Machine: MacBook Pro 2019</div>
<div class="">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 class="">PETSc: Petsc Release Version 3.16.1, Nov 01, 2021</div>
<div class="">MPI: MPICH 3.4.2</div>
<div class="">Compiler: clang-12</div>
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<div class="">Call stack (not sure how relevant that is since it is from opt version):</div>
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<div class=""><font style="font-family:monospace" class="">* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0xc)</font></div>
<div class=""><font style="font-family:monospace" class=""> frame #0: 0x0000000102303ba9 libpetsc.3.16.dylib`DMView_PlexExodusII(dm=<unavailable>, viewer=<unavailable>) at plexexodusii.c:457:45 [opt]</font></div>
<div class=""><font style="font-family:monospace" class=""> 454 else if (degree == 2) nodes[cs] = nodesHexP2;</font></div>
<div class=""><font style="font-family:monospace" class=""> 455 }</font></div>
<div class=""><font style="font-family:monospace" class=""> 456 /* Compute the number of cells not in the connectivity table */</font></div>
<div class=""><font style="font-family:monospace" class="">-> 457 cellsNotInConnectivity -= nodes[cs][3]*csSize;</font></div>
<div class=""><font style="font-family:monospace" class=""> 458</font></div>
<div class=""><font style="font-family:monospace" class=""> 459 ierr = ISRestoreIndices(stratumIS, &cells);CHKERRQ(ierr);</font></div>
<div class=""><font style="font-family:monospace" class=""> 460 ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);</font></div>
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<div class=""><font style="font-family:arial, sans-serif" class="">With regards,</font></div>
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<div class=""><font style="font-family:arial, sans-serif" class="">David Andrs</font></div>
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<div class=""><exo2.c></div>
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<div class="">-- </div>
<div class="">Professor, Department of Mathematics & Statistics</div>
<div class="">Hamilton Hall room 409A, McMaster University</div>
<div class="">1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada </div>
<div class="">Tel. +1 (905) 525 9140 ext. 27243</div>
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Professor, Department of Mathematics & Statistics<br class="">
Hamilton Hall room 409A, McMaster University<br class="">
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada <br class="">
Tel. +1 (905) 525 9140 ext. 27243</div>
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