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<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Hi Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Thank you for your help with this missing information. This solved the issue. Looking at the manual again for DMPlexBuildFromCellListParallel (internal function being called,
<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/DMPlex/DMPlexBuildFromCellListParallel/__;!!G_uCfscf7eWS!fmyMzLlbHCS_e22XlTJPzQcOaVEWo_GQ0mCMiB_G5VBovdxOfFs0mqg7g_0rox9TP8iRN_VBCeL74-xIX_Zf1aPcEnI03ePX$">
https://petsc.org/release/manualpages/DMPlex/DMPlexBuildFromCellListParallel/</a>), it did state that: “Each process owns a chunk of numVertices
<b>consecutive vertices</b>.”, which may be implying what you said, and I missed that important information.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Chonglin<o:p></o:p></span></p>
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<b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Mark Adams <mfadams@lbl.gov><br>
<b>Date: </b>Monday, October 6, 2025 at 5:27</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black"> </span><span style="font-size:12.0pt;color:black">PM<br>
<b>To: </b>Zhang, Chonglin <chonglin.zhang@und.edu><br>
<b>Cc: </b>PETSc User Mailing List <petsc-users@mcs.anl.gov><br>
<b>Subject: </b>Re: [petsc-users] Help with DMPlexCreateFromCellListParallelPetsc<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt">I think you need to reorder your points according to each processor.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt">If process 0 has 4 vertices, they will be numbered (0, 1, 2, 3), and if proc 1 has one vertex it will be 4.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt">So, to fix this, switch vertex numbering for 2 and 4.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt">Mark<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:12.0pt">On Mon, Oct 6, 2025 at 3:40</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif"> </span><span style="font-size:12.0pt">PM Zhang, Chonglin <<a href="mailto:chonglin.zhang@und.edu">chonglin.zhang@und.edu</a>>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black">Dear PETSc developers,</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black">I have some questions on the proper use of DMPlexCreateFromCellListParallelPetsc function (<a href="https://urldefense.us/v3/__https:/petsc.org/release/manualpages/DMPlex/DMPlexCreateFromCellListParallelPetsc/__;!!G_uCfscf7eWS!YJgdfNvYGp76m3zAsH07tAaJCaPnEyuyhZdGILGu2oyhW0RSJZeX4J8-IUCVNBupO7efr7Ju5zA_5ayjZ_YkwEeCuXjIJQ2K$" target="_blank">https://petsc.org/release/manualpages/DMPlex/DMPlexCreateFromCellListParallelPetsc/</a>).
I am upgrading my code’s PETSc dependency from v3.16.6 to v3.24.0 (and v3.23.3, v3.23.6). I encountered crash with DMPlexCreateFromCellListParallelPetsc function:</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">To show the crash, I modified the following test: src/dm/impls/plex/tests/ex18.c</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">Is there anything I am doing wrong when creating DMPlex using the below mesh with this test?</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">What is the order of vertex index (of own element) going into DMPlexCreateFromCellListParallelPetsc function?</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">What is the order of own vertex coordinates going into DMPlexCreateFromCellListParallelPetsc function?</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black">Here is a detailed descriptions of what I did with ex18.c to show my issue: src/dm/impls/plex/tests/ex18.c</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">A simple 2D square mesh with 5 vertices and 4 triangles, shared by 2 MPI ranks (see the below image for the mesh, also attached file).</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">Each MPI rank owns 2 elements.</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">MPI rank 0 owns vertex indexed as: 0, 1, 3, 4; rank 1 owns vertex indexed as: 2.</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">Modified code (with updated mesh information) is attached.</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">The DM view output is also attached.</span><span style="color:black"><o:p></o:p></span></p>
<p class="m-3036584293828908185msolistparagraph" style="margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-size:10.0pt;font-family:Symbol;color:black"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;color:black">Note: the original test with 2 triangles and 2 elements was running fine.</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black"><img border="0" width="594" height="768" style="width:6.1875in;height:8.0in" id="m_-3036584293828908185Picture_x0020_1" src="cid:ii_199bb9d3c9b4ce8e91"></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black">Using this new mesh, the test crashed with the following error message:</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<span style="font-size:11.0pt">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br>
[0]PETSC ERROR: Invalid argument<br>
[0]PETSC ERROR: Mesh cell 1 of type triangle is inverted, |J| = 0.<br>
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https:/petsc.org/release/faq/__;!!G_uCfscf7eWS!YJgdfNvYGp76m3zAsH07tAaJCaPnEyuyhZdGILGu2oyhW0RSJZeX4J8-IUCVNBupO7efr7Ju5zA_5ayjZ_YkwEeCuaawmeuG$" target="_blank">
https://petsc.org/release/faq/</a> for trouble shooting.<br>
[0]PETSC ERROR: PETSc Release Version 3.24.0, unknown<br>
[0]PETSC ERROR: ./ex18 with 2 MPI process(es) and PETSC_ARCH arch-centos_kokkos on boltzmann2 by zhangc20 Mon Oct 6 14:00:48 2025<br>
[0]PETSC ERROR: Configure options: --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-shared-libraries=1 --with-debugging=no --COPTFLAGS="-g -O2 -fPIC" --CXXOPTFLAGS="-g -O2 -fPIC" --FOPTFLAGS="-g -O2 -fPIC" --with-cuda=1 --with-cuda-arch=86 --with-cudac=nvcc
--with-kokkos=1 --with-kokkos-dir=./../install/kokkos/install/ --with-kokkos-kernels=1 --with-kokkos-kernels-dir=./../install/kokkos-kernels/install/ --download-metis --download-parmetis --download-fblaslapack=1 --download-triangle --with-make-np=8 PETSC_ARCH=arch-centos_kokkos<br>
[0]PETSC ERROR: #1 DMPlexCheckGeometry() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plex.c:9630<br>
[0]PETSC ERROR: #2 DMPlexCheck() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plex.c:9807<br>
[0]PETSC ERROR: #3 DMSetFromOptions_NonRefinement_Plex() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plexcreate.c:5121<br>
[0]PETSC ERROR: #4 DMSetFromOptions_Plex() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plexcreate.c:5601<br>
[0]PETSC ERROR: #5 DMSetFromOptions() at /hdd1/dsmc/comet/comet/petsc/src/dm/interface/dm.c:907<br>
[0]PETSC ERROR: #6 CreateMesh() at ex18.c:811<br>
[0]PETSC ERROR: #7 main() at ex18.c:1527<br>
[0]PETSC ERROR: PETSc Option Table entries:<br>
[0]PETSC ERROR: -dm_plex_check_all 1 (source: command line)<br>
[0]PETSC ERROR: -dm_view ascii:dm_mesh.txt:ascii_info_detail (source: command line)<br>
[0]PETSC ERROR: -interpolate create (source: command line)<br>
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to
<a href="mailto:petsc-maint@mcs.anl.gov----------" target="_blank">petsc-maint@mcs.anl.gov----------</a><br>
Abort(62) on node 0 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0<br>
[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br>
[1]PETSC ERROR: Invalid argument<br>
[1]PETSC ERROR: Mesh cell 0 of type triangle is inverted, |J| = -0.25<br>
[1]PETSC ERROR: See <a href="https://urldefense.us/v3/__https:/petsc.org/release/faq/__;!!G_uCfscf7eWS!YJgdfNvYGp76m3zAsH07tAaJCaPnEyuyhZdGILGu2oyhW0RSJZeX4J8-IUCVNBupO7efr7Ju5zA_5ayjZ_YkwEeCuaawmeuG$" target="_blank">
https://petsc.org/release/faq/</a> for trouble shooting.<br>
[1]PETSC ERROR: PETSc Release Version 3.24.0, unknown<br>
[1]PETSC ERROR: ./ex18 with 2 MPI process(es) and PETSC_ARCH arch-centos_kokkos on boltzmann2 by zhangc20 Mon Oct 6 14:00:48 2025<br>
[1]PETSC ERROR: Configure options: --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-shared-libraries=1 --with-debugging=no --COPTFLAGS="-g -O2 -fPIC" --CXXOPTFLAGS="-g -O2 -fPIC" --FOPTFLAGS="-g -O2 -fPIC" --with-cuda=1 --with-cuda-arch=86 --with-cudac=nvcc
--with-kokkos=1 --with-kokkos-dir=./../install/kokkos/install/ --with-kokkos-kernels=1 --with-kokkos-kernels-dir=./../install/kokkos-kernels/install/ --download-metis --download-parmetis --download-fblaslapack=1 --download-triangle --with-make-np=8 PETSC_ARCH=arch-centos_kokkos<br>
[1]PETSC ERROR: #1 DMPlexCheckGeometry() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plex.c:9630<br>
[1]PETSC ERROR: #2 DMPlexCheck() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plex.c:9807<br>
[1]PETSC ERROR: #3 DMSetFromOptions_NonRefinement_Plex() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plexcreate.c:5121<br>
[1]PETSC ERROR: #4 DMSetFromOptions_Plex() at /hdd1/dsmc/comet/comet/petsc/src/dm/impls/plex/plexcreate.c:5601<br>
[1]PETSC ERROR: #5 DMSetFromOptions() at /hdd1/dsmc/comet/comet/petsc/src/dm/interface/dm.c:907<br>
[1]PETSC ERROR: #6 CreateMesh() at ex18.c:811<br>
[1]PETSC ERROR: #7 main() at ex18.c:1527<br>
[1]PETSC ERROR: PETSc Option Table entries:<br>
[1]PETSC ERROR: -dm_plex_check_all 1 (source: command line)<br>
[1]PETSC ERROR: -dm_view ascii:dm_mesh.txt:ascii_info_detail (source: command line)<br>
[1]PETSC ERROR: -interpolate create (source: command line)<br>
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to
<a href="mailto:petsc-maint@mcs.anl.gov----------" target="_blank">petsc-maint@mcs.anl.gov----------</a><br>
Abort(62) on node 1 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black">Run script used: </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:#222222;background:white">mpirun -np 2 ./ex18 -dm_plex_check_all 1 -dm_view ascii:dm_mesh.txt:ascii_info_detail -interpolate create</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black">Thanks,</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black">Chonglin</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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