[petsc-users] Error in DMFieldComputeFaceData_DS with hex elements

Fri Jan 18 11:19:46 CST 2019

> On 18. Jan 2019, at 16:09, Matthew Knepley <knepley at gmail.com> wrote:
> 
> On Fri, Jan 18, 2019 at 7:54 AM rickcha--- via petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
> Dear petsc-team,
> 
> I ran into an error when using petscFE in combination with a hex mesh constructed with gmsh. The error message reads:
> 
> 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()

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:

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: No stored partition matching run parameters
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1227-gcd612eedf5  GIT Date: 2019-01-17 05:31:34 +0100
[0]PETSC ERROR: ./ex77 on a arch-linux2-intel named iket127138 by hartig Fri Jan 18 18:00:33 2019
[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
[0]PETSC ERROR: #1 CreateMesh() line 443 in /home/hartig/petsc/src/snes/examples/tutorials/ex77.c
[0]PETSC ERROR: #2 main() line 594 in /home/hartig/petsc/src/snes/examples/tutorials/ex77.c
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -bc_fixed 1
[0]PETSC ERROR: -bc_pressure 2
[0]PETSC ERROR: -def_petscspace_degree 2
[0]PETSC ERROR: -dim 3
[0]PETSC ERROR: -dm_refine 0
[0]PETSC ERROR: -elastMat_petscspace_degree 0
[0]PETSC ERROR: -fieldsplit_deformation_ksp_type preonly
[0]PETSC ERROR: -fieldsplit_deformation_pc_type lu
[0]PETSC ERROR: -fieldsplit_pressure_ksp_rtol 1e-10
[0]PETSC ERROR: -fieldsplit_pressure_pc_type jacobi
[0]PETSC ERROR: -interpolate 1
[0]PETSC ERROR: -ksp_converged_reason
[0]PETSC ERROR: -ksp_monitor_short
[0]PETSC ERROR: -ksp_rtol 1e-10
[0]PETSC ERROR: -ksp_type fgmres
[0]PETSC ERROR: -pc_fieldsplit_schur_factorization_type upper
[0]PETSC ERROR: -pc_fieldsplit_type schur
[0]PETSC ERROR: -pc_type fieldsplit
[0]PETSC ERROR: -pres_petscspace_degree 1
[0]PETSC ERROR: -run_type full
[0]PETSC ERROR: -show_solution 0
[0]PETSC ERROR: -simplex 0
[0]PETSC ERROR: -snes_converged_reason
[0]PETSC ERROR: -snes_monitor_short
[0]PETSC ERROR: -snes_rtol 1e-05
[0]PETSC ERROR: -test_partition
[0]PETSC ERROR: -wall_pres_petscspace_degree 0
[0]PETSC ERROR: -wall_pressure 0.4
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=62
:
system msg for write_line failure : Bad file descriptor

> just ot make sure your physics works? Then we can look at the GMsh file (I hate that program).
>  
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Petsc has generated inconsistent data
> [0]PETSC ERROR: Not implemented yet
> 
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1227-gcd612eedf5  GIT Date: 2019-01-17 05:31:34 +0100
> [0]PETSC ERROR: ./standaloneFEM on a arch-linux2-intel-debug named iket127138 by hartig Fri Jan 18 10:49:52 2019
> [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
> [0]PETSC ERROR: #1 DMFieldComputeFaceData_DS() line 943 in /home/hartig/petsc/src/dm/field/impls/ds/dmfieldds.c
> [0]PETSC ERROR: #2 DMFieldCreateFEGeom() line 537 in /home/hartig/petsc/src/dm/field/interface/dmfield.c
> [0]PETSC ERROR: #3 DMSNESGetFEGeom() line 2598 in /home/hartig/petsc/src/dm/impls/plex/plexfem.c
> [0]PETSC ERROR: #4 DMPlexComputeBdResidual_Single_Internal() line 1520 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c
> [0]PETSC ERROR: #5 DMPlexComputeBdResidual_Internal() line 1649 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c
> [0]PETSC ERROR: #6 DMPlexComputeResidual_Internal() line 1946 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c
> [0]PETSC ERROR: #7 DMPlexTSComputeIFunctionFEM() line 206 in /home/hartig/petsc/src/ts/utils/dmplexts.c
> [0]PETSC ERROR: #8 ComputeI2FunctionWithInertia() line 1284 in /home/hartig/cimply/femanalysis.c
> [0]PETSC ERROR: #9 TSComputeI2Function() line 1707 in /home/hartig/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: #10 SNESTSFormFunction_Alpha() line 339 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c
> [0]PETSC ERROR: #11 SNESTSFormFunction() line 4694 in /home/hartig/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: #12 SNESComputeFunction() line 2301 in /home/hartig/petsc/src/snes/interface/snes.c
> [0]PETSC ERROR: #13 SNESSolve_NEWTONLS() line 175 in /home/hartig/petsc/src/snes/impls/ls/ls.c
> [0]PETSC ERROR: #14 SNESSolve() line 4454 in /home/hartig/petsc/src/snes/interface/snes.c
> [0]PETSC ERROR: #15 TSAlpha_SNESSolve() line 101 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c
> [0]PETSC ERROR: #16 TSAlpha_Restart() line 143 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c
> [0]PETSC ERROR: #17 TSStep_Alpha() line 217 in /home/hartig/petsc/src/ts/impls/implicit/alpha/alpha2.c
> [0]PETSC ERROR: #18 TSStep() line 3664 in /home/hartig/petsc/src/ts/interface/ts.c
> [0]PETSC ERROR: #19 TSSolve() line 3847 in /home/hartig/petsc/src/ts/interface/ts.c
> 
> 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.
> 
> 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”)
> 
> I think you are looking at the coordinate space. By default, simplex mesh use affine coordinate spaces.
>  
> and in case of the hex-mesh, I get a polynomial degree of 3.
> 
> That is strange. It should be 2.

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?

Thanks,
Max

> 
>   Thanks,
> 
>     Matt
>  
> 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.
> 
> Thanks,
> Max
> 
> 
> -- 
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
> 
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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