<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 18. Jan 2019, at 16:09, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_quote"><div dir="ltr" class="">On Fri, Jan 18, 2019 at 7:54 AM rickcha--- via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" class="">petsc-users@mcs.anl.gov</a>> wrote:<br class=""></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" class="">Dear petsc-team,<br class=""><br class="">I ran into an error when using petscFE in combination with a hex mesh constructed with gmsh. The error message reads:<br class=""></div></blockquote><div class=""><br class=""></div><div class="">Yes, I am guessing that GMsh put some crazy crap in the mesh file. Can you test it out on a hex mesh from DMPlexCreateBoxMesh()</div></div></div></div></blockquote><br class="">I tested DMPlexCreateBoxMesh() and it throws me the same error message. I tried running example 77 with -simplex 0, but it seems that tensor product elements are not available for this example:</div><div><br class=""></div><div><div><br class=""></div><div>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div><div>[0]PETSC ERROR: Invalid argument</div><div>[0]PETSC ERROR: No stored partition matching run parameters</div><div>[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" class="">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div><div>[0]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1227-gcd612eedf5 GIT Date: 2019-01-17 05:31:34 +0100</div><div>[0]PETSC ERROR: ./ex77 on a arch-linux2-intel named iket127138 by hartig Fri Jan 18 18:00:33 2019</div><div>[0]PETSC ERROR: Configure options PETSC_ARCH=arch-linux2-intel --with-debugging=false --with-cc=/home/hartig/intel/bin/icc --with-cxx=/home/hartig/intel/bin/icpc --with-fc=/home/hartig/intel/bin/ifort --download-mpich --download-ml --download-parmetis --download-metis --download-hypre --download-mumps --download-scalapack --download-triangle --download-hdf5 --download-ptscotch --download-chaco</div><div>[0]PETSC ERROR: #1 CreateMesh() line 443 in /home/hartig/petsc/src/snes/examples/tutorials/ex77.c</div><div>[0]PETSC ERROR: #2 main() line 594 in /home/hartig/petsc/src/snes/examples/tutorials/ex77.c</div><div>[0]PETSC ERROR: PETSc Option Table entries:</div><div>[0]PETSC ERROR: -bc_fixed 1</div><div>[0]PETSC ERROR: -bc_pressure 2</div><div>[0]PETSC ERROR: -def_petscspace_degree 2</div><div>[0]PETSC ERROR: -dim 3</div><div>[0]PETSC ERROR: -dm_refine 0</div><div>[0]PETSC ERROR: -elastMat_petscspace_degree 0</div><div>[0]PETSC ERROR: -fieldsplit_deformation_ksp_type preonly</div><div>[0]PETSC ERROR: -fieldsplit_deformation_pc_type lu</div><div>[0]PETSC ERROR: -fieldsplit_pressure_ksp_rtol 1e-10</div><div>[0]PETSC ERROR: -fieldsplit_pressure_pc_type jacobi</div><div>[0]PETSC ERROR: -interpolate 1</div><div>[0]PETSC ERROR: -ksp_converged_reason</div><div>[0]PETSC ERROR: -ksp_monitor_short</div><div>[0]PETSC ERROR: -ksp_rtol 1e-10</div><div>[0]PETSC ERROR: -ksp_type fgmres</div><div>[0]PETSC ERROR: -pc_fieldsplit_schur_factorization_type upper</div><div>[0]PETSC ERROR: -pc_fieldsplit_type schur</div><div>[0]PETSC ERROR: -pc_type fieldsplit</div><div>[0]PETSC ERROR: -pres_petscspace_degree 1</div><div>[0]PETSC ERROR: -run_type full</div><div>[0]PETSC ERROR: -show_solution 0</div><div>[0]PETSC ERROR: -simplex 0</div><div>[0]PETSC ERROR: -snes_converged_reason</div><div>[0]PETSC ERROR: -snes_monitor_short</div><div>[0]PETSC ERROR: -snes_rtol 1e-05</div><div>[0]PETSC ERROR: -test_partition</div><div>[0]PETSC ERROR: -wall_pres_petscspace_degree 0</div><div>[0]PETSC ERROR: -wall_pressure 0.4</div><div>[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to <a href="mailto:petsc-maint@mcs.anl.gov" class="">petsc-maint@mcs.anl.gov</a>----------</div><div>application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0</div><div>[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=62</div><div>:</div><div>system msg for write_line failure : Bad file descriptor</div><div><br class=""></div><div><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="gmail_quote"><div class="">just ot make sure your physics works? Then we can look at the GMsh file (I hate that program).</div><div class=""> </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" class="">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br class="">[0]PETSC ERROR: Petsc has generated inconsistent data<br class="">[0]PETSC ERROR: Not implemented yet<br class=""><br class="">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank" class="">http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.<br class="">[0]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1227-gcd612eedf5 GIT Date: 2019-01-17 05:31:34 +0100<br class="">[0]PETSC ERROR: ./standaloneFEM on a arch-linux2-intel-debug named iket127138 by hartig Fri Jan 18 10:49:52 2019<br class="">[0]PETSC ERROR: Configure options PETSC_ARCH=arch-linux2-intel-debug --with-debugging=true --with-cc=/home/hartig/intel/bin/icc --with-cxx=/home/hartig/intel/bin/icpc --with-fc=/home/hartig/intel/bin/ifort --download-mpich --download-ml --download-parmetis --download-metis --download-hypre --download-mumps --download-scalapack --download-triangle --download-hdf5 --download-ptscotch --download-chaco<br class="">[0]PETSC ERROR: #1 DMFieldComputeFaceData_DS() line 943 in /home/hartig/petsc/src/dm/field/impls/ds/dmfieldds.c<br class="">[0]PETSC ERROR: #2 DMFieldCreateFEGeom() line 537 in /home/hartig/petsc/src/dm/field/interface/dmfield.c<br class="">[0]PETSC ERROR: #3 DMSNESGetFEGeom() line 2598 in /home/hartig/petsc/src/dm/impls/plex/plexfem.c<br class="">[0]PETSC ERROR: #4 DMPlexComputeBdResidual_Single_Internal() line 1520 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c<br class="">[0]PETSC ERROR: #5 DMPlexComputeBdResidual_Internal() line 1649 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c<br class="">[0]PETSC ERROR: #6 DMPlexComputeResidual_Internal() line 1946 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c<br class="">[0]PETSC ERROR: #7 DMPlexTSComputeIFunctionFEM() line 206 in /home/hartig/petsc/src/ts/utils/dmplexts.c<br class="">[0]PETSC ERROR: #8 ComputeI2FunctionWithInertia() line 1284 in /home/hartig/cimply/femanalysis.c<br class="">[0]PETSC ERROR: #9 TSComputeI2Function() line 1707 in /home/hartig/petsc/src/ts/interface/ts.c<br class="">[0]PETSC ERROR: #10 SNESTSFormFunction_Alpha() line 339 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c<br class="">[0]PETSC ERROR: #11 SNESTSFormFunction() line 4694 in /home/hartig/petsc/src/ts/interface/ts.c<br class="">[0]PETSC ERROR: #12 SNESComputeFunction() line 2301 in /home/hartig/petsc/src/snes/interface/snes.c<br class="">[0]PETSC ERROR: #13 SNESSolve_NEWTONLS() line 175 in /home/hartig/petsc/src/snes/impls/ls/ls.c<br class="">[0]PETSC ERROR: #14 SNESSolve() line 4454 in /home/hartig/petsc/src/snes/interface/snes.c<br class="">[0]PETSC ERROR: #15 TSAlpha_SNESSolve() line 101 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c<br class="">[0]PETSC ERROR: #16 TSAlpha_Restart() line 143 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c<br class="">[0]PETSC ERROR: #17 TSStep_Alpha() line 217 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c<br class="">[0]PETSC ERROR: #18 TSStep() line 3664 in /home/hartig/petsc/src/ts/interface/ts.c<br class="">[0]PETSC ERROR: #19 TSSolve() line 3847 in /home/hartig/petsc/src/ts/interface/ts.c<br class=""><br class="">Upon investigation, I found that petsc throws the error message because coneSize has a value of six. This is the first thing that puzzles me. I would have expected a cone size of 4 since we are dealing with faces of hex elements. Is it possible that we are on the wrong “level” of the mesh graph somehow? Printing "numFaces“ in the debugger, I get the total number of elements (not 2D faces) I have in my mesh for the hex-case.<br class=""><br class="">I ran the same case with a simplex mesh and found another thing I don’t quite understand: Both times I ran with -petscspace-degree 2. Yet in case of the simplex mesh, I get a polynomial degree of 1 in DMFieldComputeFaceData_DS (“maxDegree”)</div></blockquote><div class=""><br class=""></div><div class="">I think you are looking at the coordinate space. By default, simplex mesh use affine coordinate spaces.</div><div class=""> </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" class=""> and in case of the hex-mesh, I get a polynomial degree of 3.</div></blockquote><div class=""><br class=""></div><div class="">That is strange. It should be 2.</div></div></div></div></blockquote><div><br class=""></div>I can’t quite follow you here. Do you refer to the local coordinate system of the element used to define the shape functions? Then a degree of 1 would mean two non-collinear vectors e_1 and e_2?</div><div><br class=""></div><div>Thanks,</div><div>Max</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="gmail_quote"><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </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" class=""> In both cases I would have expected the degree to be 2, corresponding to Tet10 and Hex20 elements. I might be confusing two different concepts here. But this was how I understood the documentation until now.<br class=""><br class="">Thanks,<br class="">Max</div></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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