<div dir="ltr"><div dir="ltr">On Wed, Jan 15, 2020 at 3:47 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">
<div>
<div style="word-wrap:break-word">
<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>
<div><br>
</div>
<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>
<div><br>
</div>
<div>Attached is the sample code to reproduce the error and below is the screen output.</div></div></div></blockquote><div><br></div><div>Cool. I will run it and figure out the problem.</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><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 <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">
https://www.mcs.anl.gov/petsc/documentation/faq.html</a> 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>
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<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>
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--<span> </span><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>
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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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</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>