Info    : Running './runtime/lnx86_64/bin/gmsh /home/wayne/amoeba/svn/trunk/try3.geo -3 -format msh -saveall -smooth 3 -o /home/wayne/amoeba/svn/trunk/try3-out.gmsh' [1 node(s), max. 1 thread(s)]
Info    : Started on Mon Mar 26 13:05:25 2012
Info    : Reading '/home/wayne/amoeba/svn/trunk/try3.geo'...
Info    : Reading '/home/wayne/amoeba/svn/trunk/try3-geom.gmsh'...
Info    : 1333 vertices
Info    : Vertex numbering is dense
Info    : 2288 elements
Info    : Done reading '/home/wayne/amoeba/svn/trunk/try3-geom.gmsh'
Info    : Refining mesh...
Info    : Meshing order 2, curvilinear ON...
Info    : Meshing curves order 2...
Info    : Meshing surfaces order 2...
Info    : highOrderTools has been set up : 4734 nodes are considered
Info    : Meshing volumes order 2...
Info    : Final mesh : Worst Face Distorsion Mapping 1 Gamma 0.000550169 Nb elem. (0<d<0.2) = 0
Info    : Done meshing order 2 (0 s)
Info    : Done refining mesh (0.01 s)
Info    : Creating topology from mesh...
Info    : Removing duplicate mesh vertices...
Info    : Removed 233 duplicate mesh vertices
Info    : Done removing duplicate mesh vertices
Info    : Done creating topology from mesh (0.09 s)
Info    : Done reading '/home/wayne/amoeba/svn/trunk/try3.geo'
Info    : Meshing 1D...
Info    : Meshing curve 34 (Compound curve)
Info    : Meshing curve 38 (Compound curve)
Info    : Meshing curve 39 (Compound curve)
Info    : Meshing curve 40 (Compound curve)
Info    : Meshing curve 41 (Compound curve)
Info    : Meshing curve 42 (Compound curve)
Info    : Done meshing 1D (0 s)
Info    : Meshing 2D...
Info    : Meshing surface 35 (Compound surface, MeshAdapt)
Info    : Parametrizing surface 35 with 'harmonic map'
Info    : --- Flipping : applying cavity checks.
Info    : --- Flipping : no more flips (7 iter)
Info    : Meshing surface 36 (Compound surface, MeshAdapt)
Info    : Parametrizing surface 36 with 'harmonic map'
Info    : Meshing surface 37 (Compound surface, MeshAdapt)
Info    : Parametrizing surface 37 with 'harmonic map'
Info    : --- Flipping : applying cavity checks.
Info    : --- Flipping : no more flips (6 iter)
Info    : Meshing surface 43 (Compound surface, MeshAdapt)
Info    : Parametrizing surface 43 with 'harmonic map'
Info    : Done meshing 2D (1.87 s)
Info    : Meshing 3D...
Info    : Meshing volume 1 (Delaunay)
Error   : Self intersecting surface mesh, computing intersections (this could take a while)
Error   : Surface mesh is wrong, cannot do the 3D mesh
Constructing Delaunay tetrahedralization.
Warning:  Point 307 is identical with point 165.
Warning:  Point 143 is identical with point 114.
Delaunay seconds:  0.11
Creating surface mesh.
Error:  Invalid PLC.
  Facet (41, 172, 188) (3749) is not a valid polygon.
Constructing Delaunay tetrahedralization.
  Creating initial tetrahedralization.
  Incrementally inserting points.
Warning:  Point 307 is identical with point 165.
Warning:  Point 143 is identical with point 114.
  29084 Flips (T23 11223, T32 8120, T22 9741, T44 0)
Delaunay seconds:  0.1
Creating surface mesh.
  Constructing mapping from indices to points.
  Constructing mapping from points to tetrahedra.
Error:  Invalid PLC.
  Facet (41, 172, 188) (3749) is not a valid polygon.
Info    : Done meshing 3D (0.22 s)
Info    : 8147 vertices 16808 elements
Error   : ------------------------------
Error   : Mesh generation error summary
Error   :     0 warnings
Error   :     2 errors
Error   : Check the full log for details
Error   : ------------------------------
Info    : Writing '/home/wayne/amoeba/svn/trunk/try3-out.gmsh'...
Info    : Done writing '/home/wayne/amoeba/svn/trunk/try3-out.gmsh'
Info    : Stopped on Mon Mar 26 13:05:27 2012