[Gmsh] Segfault at partitionning / 2.12 freshly compiled

[Vincent Huber]

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 <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
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