<div dir="ltr"><div dir="ltr">On Mon, Jan 27, 2020 at 9:57 PM 'Bisht, Gautam' via tdycores-dev <<a href="mailto:tdycores-dev@googlegroups.com">tdycores-dev@googlegroups.com</a>> wrote:<br></div><div class="gmail_quote"><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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Hi Matt,
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</div>
<div>Could you issue MR to get changes from knepley/fix-dm-g2n-serial into PETSc master? I’m having some trouble during PETSc installation withexodusii using your branch, but the master seems fine.</div></div></blockquote><div><br></div><div>Yep, just submitted the MR. Should be in soon.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">
<div>Thanks,</div>
<div>-Gautam.</div>
<div>
<div><br>
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<div>On Jan 18, 2020, at 11:19 AM, 'Bisht, Gautam' via tdycores-dev <<a href="mailto:tdycores-dev@googlegroups.com" target="_blank">tdycores-dev@googlegroups.com</a>> wrote:</div>
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<div>Hi Matt,</div>
<div><br>
</div>
<div>Thanks for the fixes to the example.</div>
<div><br>
</div>
<div>-Gautam<br>
<div><br>
<blockquote type="cite">
<div>On Jan 15, 2020, at 7:05 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
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<div dir="ltr">On Wed, Jan 15, 2020 at 4:08 PM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
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<div dir="ltr">On Wed, Jan 15, 2020 at 3:47 PM 'Bisht, Gautam' via tdycores-dev <<a href="mailto:tdycores-dev@googlegroups.com" target="_blank">tdycores-dev@googlegroups.com</a>> wrote:<br>
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<div>Hi Matt,</div>
<div><br>
</div>
<div>I’m running into error while using DMPlexNaturalToGlobalBegin/End and am hoping you have some insights in what I’m doing incorrectly. I create a 2x2x2 grid and distribute it across processors (N=1,2). I create a natural and a global vector; and
then call DMPlexNaturalToGlobalBegin/End. Here are the two issues:</div>
<div><br>
</div>
<div>- When N = 1, PETSc complains about DMSetUseNatural() not being called before DMPlexDistribute(), which is certainly not the case.</div>
<div>- For N=1 and 2, global vector doesn’t have valid entries.</div>
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<div>I’m not sure how to create the natural vector and have used DMCreateGlobalVector() to create the natural vector, which could be the issue.</div>
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<div>Attached is the sample code to reproduce the error and below is the screen output.</div>
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<div>Cool. I will run it and figure out the problem.</div>
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<div>1) There was bad error reporting there. I am putting the fix in a new branch. It did not check for being on one process. If you run with</div>
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<div> knepley/fix-dm-g2n-serial</div>
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<div> It will work correctly in serial.</div>
<div><br>
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<div>2) The G2N needs a serial data layout to work, so you have to make a Section _before_ distributing. I need to put that in the docs. I have</div>
<div> fixed your example to do this and attached it. I run it with</div>
<div><br>
</div>
<div> <span style="font-family:Menlo;font-size:11px">master *:~/Downloads/tmp/Gautam$ /PETSc3/petsc/bin/mpiexec -n 1 ./ex_test -dm_plex_box_faces 2,2,2 -dm_view</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
DM Object: 1 MPI processes</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: plex</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
DM_0x84000000_0 in 3 dimensions:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>0-cells: 27</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>1-cells: 54</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>2-cells: 36</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>3-cells: 8</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Labels:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>marker: 1 strata with value/size (1 (72))</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>Face Sets: 6 strata with value/size (6 (4), 5 (4), 3 (4), 4 (4), 1 (4), 2 (4))</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Field p:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>adjacency FVM++</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Natural vector:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Vec Object: 1 MPI processes</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: seq</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
0.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
1.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
2.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
3.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
4.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
5.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
6.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
7.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Global vector:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Vec Object: 1 MPI processes</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: seq</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
0.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
1.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
2.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
3.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
4.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
5.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
6.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
7.</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Information about the mesh:</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 00; (0.250000, 0.250000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 01; (0.750000, 0.250000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 02; (0.250000, 0.750000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 03; (0.750000, 0.750000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 04; (0.250000, 0.250000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 05; (0.750000, 0.250000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 06; (0.250000, 0.750000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 07; (0.750000, 0.750000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<br>
</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
master *:~/Downloads/tmp/Gautam$ /PETSc3/petsc/bin/mpiexec -n 2 ./ex_test -dm_plex_box_faces 2,2,2 -dm_view</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
DM Object: Parallel Mesh 2 MPI processes</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: plex</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Parallel Mesh in 3 dimensions:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>0-cells: 27 27</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>1-cells: 54 54</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>2-cells: 36 36</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>3-cells: 8 8</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Labels:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>marker: 1 strata with value/size (1 (72))</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>Face Sets: 6 strata with value/size (1 (4), 2 (4), 3 (4), 4 (4), 5 (4), 6 (4))</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Field p:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>adjacency FVM++</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Natural vector:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Vec Object: 2 MPI processes</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: mpi</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Process [0]</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
0.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
1.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
2.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
3.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Process [1]</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
4.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
5.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
6.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
7.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Global vector:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Vec Object: 2 MPI processes</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span> <span> </span></span>type: mpi</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Process [0]</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
2.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
3.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
6.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
7.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Process [1]</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
0.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
1.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
4.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
5.</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
Information about the mesh:</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 00; (0.250000, 0.750000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 01; (0.750000, 0.750000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 02; (0.250000, 0.750000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 03; (0.750000, 0.750000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 04; (0.250000, 0.250000, 0.250000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 05; (0.750000, 0.250000, 0.250000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 06; (0.250000, 0.250000, 0.750000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[0] cell = 07; (0.750000, 0.250000, 0.750000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 00; (0.250000, 0.250000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 01; (0.750000, 0.250000, 0.250000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 02; (0.250000, 0.250000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 03; (0.750000, 0.250000, 0.750000); is_local = 1</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 04; (0.250000, 0.750000, 0.250000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 05; (0.750000, 0.750000, 0.250000); is_local = 0</div>
<div style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 06; (0.250000, 0.750000, 0.750000); is_local = 0</div>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
[1] cell = 07; (0.750000, 0.750000, 0.750000); is_local = 0</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_quote">
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="word-wrap:break-word">
<div>>make ex_test</div>
<div>
<div><br>
</div>
<div>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</div>
<div>>$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -np 1 ./ex_test</div>
<div>Natural vector:</div>
<div><br>
</div>
<div>Vec Object: 1 MPI processes</div>
<div> type: seq</div>
<div>0.</div>
<div>1.</div>
<div>2.</div>
<div>3.</div>
<div>4.</div>
<div>5.</div>
<div>6.</div>
<div>7.</div>
<div>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Object is in wrong state</div>
<div>[0]PETSC ERROR: DM global to natural SF was not created.</div>
<div>You must call DMSetUseNatural() before DMPlexDistribute().</div>
<div><br>
</div>
<div>[0]PETSC ERROR: See<span> </span><a href="https://protect2.fireeye.com/v1/url?k=49ab253e-151e1a87-49ab0f2b-0cc47adc5fce-24c0c8c46a909b39&q=1&e=e8c1de75-1fa2-4cdd-a1a0-86a8a8811e0a&u=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fdocumentation%2Ffaq.html" target="_blank">https://www.mcs.anl.gov/petsc/documentation/faq.html</a><span> </span>for
trouble shooting.</div>
<div>[0]PETSC ERROR: Petsc Development GIT revision: v3.12.2-537-g5f77d1e0e5 GIT Date: 2019-12-21 14:33:27 -0600</div>
<div>[0]PETSC ERROR: ./ex_test on a darwin-gcc8 named WE37411 by bish218 Wed Jan 15 12:34:03 2020</div>
<div>[0]PETSC ERROR: Configure options --with-blaslapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate --download-parmetis=yes --download-metis=yes --with-hdf5-dir=/opt/local --download-zlib --download-exodusii=yes
--download-hdf5=yes --download-netcdf=yes --download-pnetcdf=yes --download-hypre=yes --download-mpich=yes --download-mumps=yes --download-scalapack=yes --with-cc=/opt/local/bin/gcc-mp-8 --with-cxx=/opt/local/bin/g++-mp-8 --with-fc=/opt/local/bin/gfortran-mp-8
--download-sowing=1 PETSC_ARCH=darwin-gcc8</div>
<div>[0]PETSC ERROR: #1 DMPlexNaturalToGlobalBegin() line 289 in /Users/bish218/projects/petsc/petsc_v3.12.2/src/dm/impls/plex/plexnatural.c</div>
<div><br>
</div>
<div>Global vector:</div>
<div><br>
</div>
<div>Vec Object: 1 MPI processes</div>
<div> type: seq</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div><br>
</div>
<div>Information about the mesh:</div>
<div><br>
</div>
<div>Rank = 0</div>
<div>local_id = 00; (0.250000, 0.250000, 0.250000); is_local = 1</div>
<div>local_id = 01; (0.750000, 0.250000, 0.250000); is_local = 1</div>
<div>local_id = 02; (0.250000, 0.750000, 0.250000); is_local = 1</div>
<div>local_id = 03; (0.750000, 0.750000, 0.250000); is_local = 1</div>
<div>local_id = 04; (0.250000, 0.250000, 0.750000); is_local = 1</div>
<div>local_id = 05; (0.750000, 0.250000, 0.750000); is_local = 1</div>
<div>local_id = 06; (0.250000, 0.750000, 0.750000); is_local = 1</div>
<div>local_id = 07; (0.750000, 0.750000, 0.750000); is_local = 1</div>
</div>
<div><br>
</div>
<div>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</div>
<div><br>
</div>
<div>>$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -np 2 ./ex_test</div>
<div>Natural vector:</div>
<div><br>
</div>
<div>Vec Object: 2 MPI processes</div>
<div> type: mpi</div>
<div>Process [0]</div>
<div>0.</div>
<div>1.</div>
<div>2.</div>
<div>3.</div>
<div>Process [1]</div>
<div>4.</div>
<div>5.</div>
<div>6.</div>
<div>7.</div>
<div><br>
</div>
<div>Global vector:</div>
<div><br>
</div>
<div>Vec Object: 2 MPI processes</div>
<div> type: mpi</div>
<div>Process [0]</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>Process [1]</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div>0.</div>
<div><br>
</div>
<div>Information about the mesh:</div>
<div><br>
</div>
<div>Rank = 0</div>
<div>local_id = 00; (0.250000, 0.750000, 0.250000); is_local = 1</div>
<div>local_id = 01; (0.750000, 0.750000, 0.250000); is_local = 1</div>
<div>local_id = 02; (0.250000, 0.750000, 0.750000); is_local = 1</div>
<div>local_id = 03; (0.750000, 0.750000, 0.750000); is_local = 1</div>
<div>local_id = 04; (0.250000, 0.250000, 0.250000); is_local = 0</div>
<div>local_id = 05; (0.750000, 0.250000, 0.250000); is_local = 0</div>
<div>local_id = 06; (0.250000, 0.250000, 0.750000); is_local = 0</div>
<div>local_id = 07; (0.750000, 0.250000, 0.750000); is_local = 0</div>
<div><br>
</div>
<div>Rank = 1</div>
<div>local_id = 00; (0.250000, 0.250000, 0.250000); is_local = 1</div>
<div>local_id = 01; (0.750000, 0.250000, 0.250000); is_local = 1</div>
<div>local_id = 02; (0.250000, 0.250000, 0.750000); is_local = 1</div>
<div>local_id = 03; (0.750000, 0.250000, 0.750000); is_local = 1</div>
<div>local_id = 04; (0.250000, 0.750000, 0.250000); is_local = 0</div>
<div>local_id = 05; (0.750000, 0.750000, 0.250000); is_local = 0</div>
<div>local_id = 06; (0.250000, 0.750000, 0.750000); is_local = 0</div>
<div>local_id = 07; (0.750000, 0.750000, 0.750000); is_local = 0</div>
<div><br>
</div>
<div>
<div>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-Gautam</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div style="word-wrap:break-word"></div>
<div style="word-wrap:break-word"><br>
<div><br>
<blockquote type="cite">
<div>On Jan 9, 2020, at 4:57 PM, 'Bisht, Gautam' via tdycores-dev <<a href="mailto:tdycores-dev@googlegroups.com" target="_blank">tdycores-dev@googlegroups.com</a>> wrote:</div>
<br>
<div>
<div style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
<br>
<blockquote type="cite">
<div>On Jan 9, 2020, at 4:25 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div dir="ltr">On Thu, Jan 9, 2020 at 1:35 PM 'Bisht, Gautam' via tdycores-dev <<a href="mailto:tdycores-dev@googlegroups.com" target="_blank">tdycores-dev@googlegroups.com</a>> wrote:<br>
</div>
<div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
> On Jan 9, 2020, at 2:58 PM, Jed Brown <<a href="mailto:jed@jedbrown.org" target="_blank">jed@jedbrown.org</a>> wrote:<br>
><span> </span><br>
> "'Bisht, Gautam' via tdycores-dev" <<a href="mailto:tdycores-dev@googlegroups.com" target="_blank">tdycores-dev@googlegroups.com</a>> writes:<br>
><span> </span><br>
>>> Do you need to rely on the element number, or would coordinates (of a<br>
>>> centroid?) be sufficient for your purposes? <span> </span><br>
>><span> </span><br>
>> I do need to rely on the element number. In my case, I have a mapping file that remaps data from one grid onto another grid. Though I’m currently creating a hexahedron mesh, in the future I would be reading in an unstructured grid from a file for which
I cannot rely on coordinates.<br>
><span> </span><br>
> How does the mapping file work and how is it generated?<br>
<br>
In CESM/E3SM, the mapping file is used to map fluxes or states between grids of two components (e.g. land & atmosphere). The mapping method can be conservative, nearest neighbor, bilinear, etc. While CESM/E3SM uses ESMF_RegridWeightGen to generate the mapping
file, I’m using by own MATLAB script to create the mapping file.<br>
<br>
I’m surprised that this is not an issue for other codes that are using DMPlex. E.g In PFLOTRAN, when a user creates a custom unstructured grid, they can specify material property for each grid cell. So, there should be a way to create a vectorscatter that will
scatter material property read in the “application”-order (i.e. order before calling DMPlexDistribute() ) to ghosted-order (i.e. order after calling DMPlexDistribute()).<br>
</blockquote>
<div><br>
</div>
<div>We did build something specific for this because some people wanted it. I wish I could purge this from all simulations. Its </div>
<div>definitely destructive, but this is the way the world currently is.</div>
<div><br>
</div>
<div>You want this:</div>
<div><br>
</div>
<div> <a href="https://protect2.fireeye.com/v1/url?k=5fd6bd0b-036383c4-5fd6971e-0cc47adc5e60-2156f2075f6da02c&q=1&e=986b333d-b320-4f42-9c3c-fd4c4b3e0e40&u=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-current%2Fdocs%2Fmanualpages%2FDMPLEX%2FDMPlexNaturalToGlobalBegin.html" target="_blank">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexNaturalToGlobalBegin.html</a></div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Perfect.</div>
<div><br>
</div>
<div>Thanks.</div>
<div>-Gautam</div>
<div><br>
</div>
<br>
<blockquote type="cite">
<div>
<div dir="ltr" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
> We can locate points and create interpolation with unstructured grids.<br>
><span> </span><br>
> --<span> </span><br>
> You received this message because you are subscribed to the Google Groups "tdycores-dev" group.<br>
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> To view this discussion on the web visit<span> </span><a href="https://protect2.fireeye.com/v1/url?k=b265c01b-eed0fed4-b265ea0e-0cc47adc5e60-1707adbf1790c7e4&q=1&e=0962f8e1-9155-4d9c-abdf-2b6481141cd0&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F8736come4e.fsf%2540jedbrown.org" rel="noreferrer" target="_blank">https://protect2.fireeye.com/v1/url?k=b265c01b-eed0fed4-b265ea0e-0cc47adc5e60-1707adbf1790c7e4&q=1&e=0962f8e1-9155-4d9c-abdf-2b6481141cd0&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F8736come4e.fsf%2540jedbrown.org</a>.<br>
<br>
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To view this discussion on the web visit<span> </span><a href="https://protect2.fireeye.com/v1/url?k=711264f2-2da75a3d-71124ee7-0cc47adc5e60-a1731ca51d9b5203&q=1&e=4ec2bd09-0f1d-461c-bde7-4a0d8446ce3d&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F9AB001AF-8857-446A-AE69-E8D6A25CB8FA%2540pnnl.gov" rel="noreferrer" target="_blank">https://groups.google.com/d/msgid/tdycores-dev/9AB001AF-8857-446A-AE69-E8D6A25CB8FA%40pnnl.gov</a>.<br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
--<span> </span><br>
<div dir="ltr">
<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>
</div>
<div style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">--<span> </span></span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
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<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>
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<div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
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<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>
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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></div>