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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Matt,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good morning from NZ! Thanks for the speedy response! That helps a lot.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I think the problem is the way I’m labelling the grid before setting up the ghost cells. I think…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When you say:<o:p></o:p></span></p>
<p class="MsoNormal">“When DMPlexConstructGhostCells() is called, it will put ghost cells on the other side of the true boundary”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Does that mean that overlap cells are labelled as ghost cells? Aren’t they on the other side of the true boundary? Or by true boundary do you mean the outer
edge of the overlap cells?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m testing the code using two different 3 cell exo files. One is the simpleblock-100.exo from the shared directory and the other is an exo made using a python
script and paraview. The simpleblock-100.exo has labels already assigned whereas the has none.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Should we be expecting the exo’s to be labelled appropriately outside of Petsc or should we check them and label them within the code? The two grids are being
labelled very differently at the moment and I’m not sure which is right of (mostly likely) if both are wrong…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks again<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">John<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">--<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Dr John O'Sullivan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Lecturer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">Department of Engineering Science<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">University of Auckland, New Zealand<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">email:
<a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev">jp.osullivan at auckland.ac.nz</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:black">tel: +64 (0)9 923 85353<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Matthew Knepley [mailto:knepley@gmail.com]
<br>
<b>Sent:</b> Thursday, 12 March 2015 3:06 a.m.<br>
<b>To:</b> John O'Sullivan<br>
<b>Cc:</b> petsc-dev@mcs.anl.gov<br>
<b>Subject:</b> Re: [petsc-dev] DMPlex, Finite Volume, overlap and ghost cells...<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Mar 11, 2015 at 3:34 AM, John O'Sullivan <<a href="mailto:jp.osullivan@auckland.ac.nz" target="_blank">jp.osullivan@auckland.ac.nz</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi all,<br>
<br>
I've managed to get myself very confused about how to use DMPlex correctly for a distributed Finite Volume grid...<br>
<br>
My understanding was that along partition boundaries the ghost cells are used store cell information from neighbouring partitions so that the fluxes can be calculated.<br>
<br>
Though debugging through ex11 it seems like overlap is set equal to 1?<br>
<br>
I'm solving a simple pressure-diffusion equation on a 1D column (from an exo grid) which works fine on a single processor but not in parallel. I'm certainly not setting things up right or labeling correctly...<br>
<br>
Could someone please explain the most appropriate way to set up and label the DM, whether the overlap should be 0 or 1 and whether ghost cells should be placed on internal partition boundaries.<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Yes, for FV the partition overlap should be 1, as it is in ex11. This means that when the partition happens, we will<o:p></o:p></p>
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<p class="MsoNormal">put a layer of cells on the other side of partition boundaries,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">When DMPlexConstructGhostCells() is called, it will put ghost cells on the other side of the true boundary. Both<o:p></o:p></p>
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<p class="MsoNormal">kinds of cells will be separated from interior cells by the DMPlexGetHybridBounds(&cMax), where cMax is the<o:p></o:p></p>
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<p class="MsoNormal">first ghost cell.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Now you still need a way to get rid of faces between ghost cells (which only occur in cells across a partition boundary).<o:p></o:p></p>
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<p class="MsoNormal">To do this, you use the "ghost" label we make during partitioning:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);<o:p></o:p></p>
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<p class="MsoNormal"> ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);<o:p></o:p></p>
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<p class="MsoNormal"> if (ghost >= 0) continue;<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">What exactly is going wrong?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Matt<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Thanks!<br>
John<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<pre><span style="color:black">--<br>Dr John O'Sullivan<o:p></o:p></span></pre>
<pre><span style="color:black">Lecturer<o:p></o:p></span></pre>
<pre><span style="color:black">Department of Engineering Science<o:p></o:p></span></pre>
<pre><span style="color:black">University of Auckland, New Zealand<o:p></o:p></span></pre>
<pre><span style="color:black">email: <a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev" target="_blank">jp.osullivan at auckland.ac.nz</a><o:p></o:p></span></pre>
<pre><span style="color:black">tel: +64 (0)9 923 85353<o:p></o:p></span></pre>
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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">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<o:p></o:p></p>
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