[Gmsh] Segfault at partitionning / 2.12 freshly compiled

Thu May 19 14:31:53 CEST 2016

Dear Pr. Geuzaine,

Thank you for your quick answer.

>From an old svn clone, I have made an update (svn up) then a build from
scratch.

./gmsh -3 -part 12 ../demos/sphere.geo runs like a charm now.

All the best,

VH.

2016-05-19 14:11 GMT+02:00 Christophe Geuzaine <cgeuzaine at ulg.ac.be>:

>
> 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
> >
> >
> > _______________________________________________
> > gmsh mailing list
> > gmsh at onelab.info
> > http://onelab.info/mailman/listinfo/gmsh
>
> --
> 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
> Free software: http://gmsh.info | http://getdp.info | http://onelab.info
>
>

-- 
Docteur Ingénieur de recherche
CeMoSiS <http://www.cemosis.fr> - vincent.huber at cemosis.fr
Tel: +33 (0)3 68 8*5 02 06*
IRMA - 7, rue René Descartes
67 000 Strasbourg
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://onelab.info/pipermail/gmsh/attachments/20160519/e3e5e182/attachment-0001.html>