[Gmsh] Segfault at partitionning / 2.12 freshly compiled

Thu May 19 14:11:21 CEST 2016

Dear Vincent,

This should be fixed in the SVN version (or recent nightly snapshots). Give it a try and let us know.

Christophe

> On 19 May 2016, at 12:10, Vincent Huber <vincent.huber at cemosis.fr> wrote:
> 
> Dear all,
> 
> I have compiled this http://gmsh.info/src/gmsh-2.12.0-source.tgz
> with
> 
> cmake \
>   -DCMAKE_CXX_COMPILER=`which g++` \
>   -DCMAKE_C_COMPILER=`which gcc` \
>   -DCMAKE_INSTALL_PREFIX=/data/software/install/gmsh-
> 2.12.0
>  \
>   -DCMAKE_BUILD_TYPE=release \
>   -DENABLE_BUILD_LIB=ON \
>   -DENABLE_BUILD_SHARED=ON \
>   -DENABLE_BUILD_DYNAMIC=ON \
>   -DENABLE_MPI=OFF \
>   -DENABLE_MUMPS=OFF \
>   -DENABLE_OPENMP=OFF  \
>   ..
> 
> The logs are at the end of the mail.
> 
> I have meshed demos/sphere.geo with:
> 
> gmsh -3
>  demos/sphere.geo
> 
> successfully.
> 
> problem here
> the partition process goes wrong:
> 
> gmsh -3 -part 3
>  demos/sphere.geo
> 
> (see logs at the end).
> 
> Please note I have successfully meshed and partitioned a mesh from the GUI.
> 
> All the best,
> 
> VH
> 
> CMake
> 
> -- Found Blas(ATLAS)
> -- Found Lapack(ATLAS)
> -- Found Mesh
> -- Found Solver
> -- Found Post
> -- Found Plugins
> -- Found Parser
> -- Found Fltk
> -- Using fltk-config script 
> for Fltk 1.3
> 
> -- Found NativeFileChooser
> -- Found ONELAB
> -- Found ONELABMetamodel
> -- Found Jpeg
> -- Found Zlib
> -- Found Png
> -- Found Mpeg
> -- Found OpenGL
> -- Found Ann
> -- Found Bfgs
> -- Found Cairo
> -- Found DIntegration
> -- Found OptHom
> -- Found Kbipack
> -- Found GMP
> -- Found MathEx
> -- Found Metis
> -- Note: By including Metis you have to comply with Metis
> ' special licensing requirements stated in contrib/Metis/README.txt.
> -- Found Chaco
> -- Found Voro3D
> -- Found Blossom
> -- Found Netgen
> -- Found Bamg
> -- System MMG3D not found: using contrib/mmg3d instead
> -- Found Mmg3d
> -- Found Tetgen(1.5)
> -- Note: By including Tetgen you have to comply with Tetgen'
> s special licensing requirements stated in
>  contrib/Tetgen*/LICENSE.
> -- System GMM not found: using contrib/gmm instead
> -- Found Gmm
> -- Found Taucs
> -- Using PETSc dir: /data/software/install/petsc-
> 3.6.3/openmpi-1.10.0
> 
> -- Using PETSc arch:
> -- Found PETSc
> -- Using SLEPc dir: /data/software/install/slepc-
> 3.6.3/openmpi-1.10.0
> 
> -- Found SLEPc
> -- Found OpenCascade
> -- Found Salome
> -- Found Dlopen
> -- Found LinuxJoystick
> --
> -- Gmsh 
> 2.12.0 has been configured for
>  Linux
> --
> --  * Build options: Ann Bamg Bfgs Blas(ATLAS) Blossom Cairo Chaco DIntegration Dlopen Fltk GMP Gmm Jpeg Kbipack Lapack(ATLAS) LinuxJoystick MathEx Mesh Metis Mmg3d Mpeg NativeFileChooser Netgen ONELAB ONELABMetamodel OpenCascade OpenGL OptHom PETSc Parser Plugins Png Post SLEPc Salome Solver Taucs Tetgen(
> 1.5
> ) Voro3D Zlib
> --  * Build 
> type
> : release
> --  * C compiler: /data/software/install/gcc-
> 4.9.0
> /bin/gcc
> --  * C++ compiler: /data/software/install/gcc-
> 4.9.0
> /bin/g++
> --  * Install prefix: /data/software/install/gmsh-
> 2.12.0
> 
> --
> -- Configuring 
> done
> 
> -- Generating 
> done
> 
> -- Build files have been written to: /data/software/src/gmsh-
> 2.12.0
> -source/build
> 
> partitioning
> 
> Info : Running ‘gmsh -3 ./demos/sphere.geo -part 3’ [Gmsh 2.12.0, 1 node, max. 1 thread]
> Info : Started on Thu May 19 12:06:01 2016
> Info : Reading ‘./demos/sphere.geo’…
> Info : Done reading ‘./demos/sphere.geo’
> Info : Meshing 1D…
> Info : Meshing curve 1 (Circle)
> Info : Meshing curve 2 (Circle)
> Info : Meshing curve 3 (Circle)
> Info : Meshing curve 4 (Circle)
> Info : Meshing curve 5 (Circle)
> Info : Meshing curve 6 (Circle)
> Info : Meshing curve 7 (Circle)
> Info : Meshing curve 8 (Circle)
> Info : Meshing curve 9 (Circle)
> Info : Meshing curve 10 (Circle)
> Info : Meshing curve 11 (Circle)
> Info : Meshing curve 12 (Circle)
> Info : Done meshing 1D (0.003091 s)
> Info : Meshing 2D…
> Info : Meshing surface 14 (Ruled surface, Frontal)
> Info : Meshing surface 16 (Ruled surface, Frontal)
> Info : Meshing surface 18 (Ruled surface, Frontal)
> Info : Meshing surface 20 (Ruled surface, Frontal)
> Info : Meshing surface 22 (Ruled surface, Frontal)
> Info : Meshing surface 24 (Ruled surface, Frontal)
> Info : Meshing surface 26 (Ruled surface, Frontal)
> Info : Meshing surface 28 (Ruled surface, Frontal)
> Info : Done meshing 2D (0.20296 s)
> Info : Meshing 3D…
> Info : Delaunay Meshing 1 volumes with 1 connected components
> Info : Meshing volume 30 (Delaunay)
> Delaunizing vertices…
> Delaunay seconds: 0.527774
> Creating surface mesh …
> Surface mesh seconds: 0.004444
> Recovering boundaries…
> Boundary recovery seconds: 0.004269
> Removing exterior tetrahedra …
> Exterior tets removal seconds: 0.000612
> Recovering Delaunayness…
> Delaunay recovery seconds: 0.146909
> Optimizing mesh…
> Optimization seconds: 0.00224
> 
> Writing nodes.
> Writing elements.
> Writing faces.
> Writing edges.
> 
> Output seconds: 0.002485
> Total running seconds: 0.68894
> 
> Statistics:
> 
> Input points: 1603
> Input facets: 3202
> Input segments: 4803
> Input holes: 0
> Input regions: 0
> 
> Mesh points: 1603
> Mesh tetrahedra: 4448
> Mesh faces: 10497
> Mesh edges: 7651
> Mesh faces on exterior boundary: 3202
> Mesh edges on exterior boundary: 4803
> Mesh faces on input facets: 3202
> Mesh edges on input segments: 4803
> 
> Info : 1603 points 7651 edges and 3202 faces in the initial mesh
> Info : Found region 30
> Info : 0 points created - Worst tet radius is 10.7622 (PTS removed 0 0)
> Info : 3D point insertion terminated (4111 points created):
> Info : - 0 Delaunay cavities modified for star shapeness
> Info : - 0 points could not be inserted
> Info : - 20740 tetrahedra created in 0.213642 sec. (97078 tets/sec.)
> Info : Done meshing 3D (0.972973 s)
> Info : 4112 vertices 24141 elements
> Info : Building graph…
> [1] 57253 segmentation fault (core dumped) gmsh -3 ./demos/sphere.geo -part 3
> 
> -- 
> Docteur Ingénieur de recherche
> CeMoSiS - vincent.huber at cemosis.fr
> Tel: +33 (0)3 68 85 02 06
> IRMA - 7, rue René Descartes
> 67 000 Strasbourg
> 
> 
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-- 
Prof. Christophe Geuzaine
University of Liege, Electrical Engineering and Computer Science 
http://www.montefiore.ulg.ac.be/~geuzaine

Tetrahedron V, July 4-5 2016: http://tetrahedron.montefiore.ulg.ac.be
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