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<div>Jesus,<br>
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<div>The CGNS files we get from Pointwise have only one base, so that should not be an issue. However, sections are needed to contain each cell type, the BCs, and zonal boundaries. So, there are always several sections. The grid that Spencer made for you
must have multiple sections. We have to be able to deal with grids like Spencer's example or else it's not useful.</div>
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<div>B.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size: 11pt;" color="#000000" data-ogsc=""><b>From:</b> Ferrand, Jesus A. <FERRANJ2@my.erau.edu><br>
<b>Sent:</b> Monday, January 16, 2023 5:41 PM<br>
<b>To:</b> petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject:</b> DMPlex and CGNS</font>
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<div class="x_elementToProof"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Dear PETSc team:</span></div>
<div class="x_elementToProof"><span style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="x_elementToProof"><span class="x_ContentPasted2" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">I would like to use DMPlex to partition a mesh stored as a CGNS file.
I configured my installation with --download_cgns = 1, got me a .cgns file and called DMPlexCreateCGNSFromFile() on it. Doing so got me this error:<br>
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<div class="x_elementToProof"><span class="x_ContentPasted1 x_ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">[0]PETSC ERROR: --------------------- Error Message
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<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: Error in external library</div>
<div class="x_FluidPluginCopy x_ContentPasted3"><b>[0]PETSC ERROR: CGNS file must have a single section, not 4</b></div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: Petsc Release Version 3.18.3, unknown
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<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: ./program.exe on a arch-linux-c-debug named F86 by jesus Mon Jan 16 17:25:11 2023</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: Configure options --download-mpich=yes --download-hdf5=yes --download-cgns=yes --download-metis=yes --download-parmetis=yes --download-ptscotch=yes --download-chaco=yes --with-32bits-pci-domain=1</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: #1 DMPlexCreateCGNS_Internal() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/cgns/plexcgns2.c:104</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: #2 DMPlexCreateCGNS() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexcgns.c:60</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: #3 DMPlexCreateCGNSFromFile_Internal() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/cgns/plexcgns2.c:27</div>
<div class="x_FluidPluginCopy x_ContentPasted3">[0]PETSC ERROR: #4 DMPlexCreateCGNSFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexcgns.c:29</div>
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<div class="x_elementToProof"><span class="x_ContentPasted1 x_ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
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<div class="x_elementToProof"><span class="x_ContentPasted1 x_ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">I looked around mail archives for clused and found
this one (</span><span class="x_ContentPasted0" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><a href="https://lists.mcs.anl.gov/pipermail/petsc-users/2018-June/035544.html" data-auth="NotApplicable" id="LPlnk715632" data-ogsc="" style="">https://lists.mcs.anl.gov/pipermail/petsc-users/2018-June/035544.html</a>).
There, Matt provides a link to the source code for <span class="x_FluidPluginCopy" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><span class="x_FluidPluginCopy" style="background-color: rgb(255, 255, 255);"><span class="x_FluidPluginCopy x_ContentPasted7" style="background-color: rgb(255, 255, 255);">DMPlexCreateCGNSFromFile()</span></span></span>
and another (seemingly broken) link to CGNS files that can be opened with the former<span class="x_FluidPluginCopy" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><span class="x_FluidPluginCopy x_ContentPasted5" style="background-color: rgb(255, 255, 255);"></span></span>.
After reading the source code I now understand that <span class="x_FluidPluginCopy x_ContentPasted4" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
it </span>is hardcoded for CGNS files that feature a single "base" and a single "section", whatever those are.
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<div class="x_elementToProof"><span class="x_ContentPasted0" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="x_elementToProof"><span class="x_ContentPasted0" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">After navigating the CGNS documentation, I can sympathize with the
comments in the source code.<br>
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<div class="x_elementToProof"><span class="x_ContentPasted0" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
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<div class="x_elementToProof"><span class="x_ContentPasted0" style="font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Anyhow, I wanted to ask if I could be furnished with one such CGNS
file that is compatible with <span class="x_FluidPluginCopy" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span class="x_FluidPluginCopy" style="background-color: rgb(255, 255, 255);"><span class="x_FluidPluginCopy x_ContentPasted6" style="background-color: rgb(255, 255, 255);">DMPlexCreateCGNSFromFile()</span></span></span> to see if I can modify my CGNS files
to conform to it. If not, I will look into building the DAG myself using DMPlex APIs.<br>
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<span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Sincerely:</span></p>
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<span style="margin: 0px; font-family: "Courier New", monospace; font-size: 14pt;"><b style=""><span style="font-family:"Courier New",monospace">J.A. Ferrand</span></b></span><u><span style="margin: 0px; font-family: "Swis721 BlkCn BT", sans-serif; font-size: 12pt;"></span></u></p>
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<span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Embry-Riddle Aeronautical University - Daytona Beach FL</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">M.Sc.</span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">
Aerospace Engineering <br>
</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">B.Sc.</span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">
Aerospace Engineering</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">B.Sc.</span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">
Computational Mathematics</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><span style="margin: 0px; color: rgb(0, 0, 0); font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br>
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<span style="margin: 0px; color: rgb(0, 0, 0); font-family: "Times New Roman", Times, serif; font-size: 12pt;"></span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;"></span>
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<span style="font-family:"Times New Roman",Times,serif"></span><u><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Phone:</span></u><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">
(386)-843-1829</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><u><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Email(s):</span></u><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">
ferranj2@my.erau.edu</span></p>
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<span style="font-family:"Times New Roman",Times,serif"></span><span style="margin: 0px; color: black; font-family: Courant; font-size: 12pt;"><span style="margin:0px; font-family:"Times New Roman",Times,serif">
</span></span><span style="margin: 0px; color: black; font-family: "Times New Roman", Times, serif; font-size: 12pt;">jesus.ferrand@gmail.com</span></p>
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