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On Mon, May 13, 2024 at 9: 33 PM Adrian Croucher <a. croucher@ auckland. ac. nz> wrote: hi, We often create meshes in GMSH format using the meshio library. This works OK if we stick to GMSH file format 2. 2. If we use GMSH file format 4. 1,
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<div dir="ltr"><div dir="ltr">On Mon, May 13, 2024 at 9:33 PM Adrian Croucher <<a href="mailto:a.croucher@auckland.ac.nz">a.croucher@auckland.ac.nz</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 class="msg-2675469690238010328"><u></u>
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hi, We often create meshes in GMSH format using the meshio library. This works OK if we stick to GMSH file format 2. 2. If we use GMSH file format 4. 1, DMPlex can't read them because it expects the "Entities" section to be present: [0]PETSC
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<div><pre style="font-family:sans-serif;font-size:100%;white-space:pre-wrap">hi,
We often create meshes in GMSH format using the meshio library. This
works OK if we stick to GMSH file format 2.2.
If we use GMSH file format 4.1, DMPlex can't read them because it
expects the "Entities" section to be present:
[0]PETSC ERROR: Unexpected data in file
[0]PETSC ERROR: File is not a valid Gmsh file, expecting $Entities, not
$Nodes
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZfBS1KM5EBZ7ZJIu6lBKFcclVMmXteXsW8m9HBEZ5tIf0u_3duEFt9eXKF7FcorQSAQqD5SbJrYh4C8rX676S_IMI_sp6naX$" target="_blank">https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZfBS1KM5EBZ7ZJIu6lBKFcclVMmXteXsW8m9HBEZ5tIf0u_3duEFt9eXKF7FcorQSAQqD5SbJrYh4C8rX676S_IMI_sp6naX$</a> for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision:
v3.21.1-124-g2d06e2faec8 GIT Date: 2024-05-08 19:31:33 +0000
[0]PETSC ERROR: waiwera on a main-debug named EN438880 by acro018 Tue
May 14 11:25:54 2024
[0]PETSC ERROR: Configure options --with-x --download-hdf5
--download-zlib --download-netcdf --download-pnetcdf --download-exodusii
--download-triangle --download-ptscotch --download-chaco --download-hypre
[0]PETSC ERROR: #1 GmshExpect() at
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexgmsh.c:270
[0]PETSC ERROR: #2 DMPlexCreateGmsh() at
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexgmsh.c:1608
[0]PETSC ERROR: #3 DMPlexCreateGmshFromFile() at
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexgmsh.c:1469
[0]PETSC ERROR: #4 DMPlexCreateFromFile() at
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexcreate.c:5804
By default meshio doesn't seem to write the Entities section. From what
I can gather, it is optional.
Am I right that this section is not optional in DMPlex?</pre></div></div></blockquote><div><br></div><div>I wish GMsh was clearer about what is optional: <a href="https://urldefense.us/v3/__https://gmsh.info/doc/texinfo/gmsh.html*MSH-file-format__;Iw!!G_uCfscf7eWS!fS2tI8aC3rUnGOv-LbLPj1PRyijAPB-EO54CwUBP6pNFD-VKeGE98pOHepNMSTP_krHBKTZNk92Bx01NrC-T$">https://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format</a></div><div>They do talk about it, but not exhaustively. GMsh always writes and $Entities block from what I can tell.</div><div>I can make it optional, it just might take until after the PETSc Meeting.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt </div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-2675469690238010328"><div><pre style="font-family:sans-serif;font-size:100%;white-space:pre-wrap">- Adrian
--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a href="mailto:a.croucher@auckland.ac.nz" target="_blank">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611
</pre></div>
</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fS2tI8aC3rUnGOv-LbLPj1PRyijAPB-EO54CwUBP6pNFD-VKeGE98pOHepNMSTP_krHBKTZNk92Bx_9VtYPq$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>