[Gmsh] Remesh STL

look mlook at me.com
Thu Jun 25 12:57:20 CEST 2015

Hello everybody,

I am trying to remesh a very easy trivial *.stl geometry which I previously generated in Blender. Therefore I followed the instructions from a gmsh mailing list post: http://geuz.org/pipermail/gmsh/2011/006887.html <http://geuz.org/pipermail/gmsh/2011/006887.html>

1) Open inout.stl in gmsh (with gui)
2) Click on Mesh->Reclassify 2D
3) Click on "All" in step 1 and step 3, then click on "Reclassify"
4) Save the reclassified mesh as a new msh file -> reclassified_inout.msh
5) I can see several distinct surfaces when I open this new file and go to Tools/Visibility.
6) Write a new file test.geo:

Merge "reclassified_inout.msh";


Compound Surface(23)={3};
Compound Surface(24)={4};
Compound Surface(25)={5};
Compound Surface(26)={6};
Compound Surface(27)={7};
Compound Surface(28)={8};
Compound Surface(29)={9};
Compound Surface(30)={10};
Compound Surface(31)={11};
Compound Surface(32)={12};
Compound Surface(33)={13};
Compound Surface(34)={14};
7) Run 
gmsh -2 test.geo
Unfortunately I get the following error message:
kate at kate-VirtualBox:/media/sf_documents/gmsh/Daten/inout_cubes_vonBlender$ gmsh -2 test.geo
Info    : Running 'gmsh -2 test.geo' [Gmsh 2.9.3, 1 node, max. 1 thread]
Info    : Started on Thu Jun 25 11:34:00 2015
Info    : Reading 'test.geo'...
Info    : Reading 'reclassified_inout.msh'...
Info    : 16 vertices
Info    : Vertex numbering is dense
Info    : 36 elements
Info    : Done reading 'reclassified_inout.msh'
Info    : Creating topology from mesh...
Info    : Removing duplicate mesh vertices...
Info    : Found 0 duplicate vertices 
Info    : No duplicate vertices found
Info    : Done creating topology from mesh (0.000554 s)
Info    : Done reading 'test.geo'
Info    : Meshing 1D...
Info    : Done meshing 1D (1.7e-05 s)
Info    : Meshing 2D...
Info    : Meshing surface 23 (Compound surface, MeshAdapt)
Info    : Parametrizing surface 23 with 'convex map'
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Not for unassembled matrix
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014 
[0]PETSC ERROR: gmsh on a linux_complex_mumps_seq named kate-VirtualBox by kate Thu Jun 25 11:34:00 2015
[0]PETSC ERROR: Configure options --with-pic --with-blas-lapack-lib="[/usr/local/lib/liblapack.a,/usr/local/lib/libblas.a,-lpthread]" --with-clanguage=cxx --with-debugging=0 --with-mpi=0 --with-x=0 --with-ssl=0 --with-mpiuni-fortran-binding=0 --with-mumps-include=/home/geuzaine/src/mumps_seq/include --with-mumps-lib="[/home/geuzaine/src/mumps_seq/lib/libcmumps.a,/home/geuzaine/src/mumps_seq/lib/libsmumps.a,/home/geuzaine/src/mumps_seq/lib/libdmumps.a,/home/geuzaine/src/mumps_seq/lib/libzmumps.a,/home/geuzaine/src/mumps_seq/lib/libmumps_common.a,/home/geuzaine/src/mumps_seq/lib/libmetis.a,/home/geuzaine/src/mumps_seq/lib/libmpiseq.a,/home/geuzaine/src/mumps_seq/lib/libpord.a]" --with-mumps-serial --with-shared-libraries=0 --with-scalar-type=complex
[0]PETSC ERROR: #1 MatGetOrdering() line 189 in /home/geuzaine/src/petsc-3.5.2/src/mat/order/sorder.c
[0]PETSC ERROR: #2 PCSetUp_ILU() line 196 in /home/geuzaine/src/petsc-3.5.2/src/ksp/pc/impls/factor/ilu/ilu.c
[0]PETSC ERROR: #3 PCSetUp() line 902 in /home/geuzaine/src/petsc-3.5.2/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #4 KSPSetUp() line 305 in /home/geuzaine/src/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #5 KSPSolve() line 417 in /home/geuzaine/src/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #6 _try() line 9 in /home/geuzaine/src/gmsh/Solver/linearSystemPETSc.hpp
Aborted (core dumped)
I have attached the necessary files to reproduce the problem. I tried with gmsh 2.9.3 on OS X and gmsh 2.9.3 on Ubuntu.

I would appreciate any help/hint/comment!

Best regards,

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