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CSG-3D geometry demo got wrong information

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I use FEniCS 1.2.0 with Ubuntu 13.10 and want to run the CSG-3D geometry demo as described in the FEniCS website enter link description here

and got very strange error message as follow:

Compact output of 3D geometry:
((Box(0, 0, 0, 1, 1, 1) + Cone( <Point x = 0 y = 0 z = -1>, <Point x = 0 y = 0 z = 1>, 1, 0.5 )) - Sphere(<Point x = 0 y = 0 z = 0>, 0.3))

Verbose output of 3D geometry:
<Difference>
{
  <Union>
  {
    <Box with first corner at (0, 0, 0) and second corner at (1, 1, 1)>
    <Cone with top at <Point x = 0 y = 0 z = -1>, top radius 1 and bottom at <Point x = 0 y = 0 z = 1>, bottom radius 0.5, with 32 slices>
  }
  <Sphere at <Point x = 0 y = 0 z = 0> with radius 0.3>
}
Convert to nef polyhedron
[zhouyi:07222] *** Process received signal ***
[zhouyi:07222] Signal: Segmentation fault (11)
[zhouyi:07222] Signal code: Address not mapped (1)
[zhouyi:07222] Failing at address: (nil)
[zhouyi:07222] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfbb0) [0x7f4e8781dbb0]
[zhouyi:07222] [ 1] /usr/lib/libdolfin.so.1.2(_ZNK4CGAL18Filtered_predicateINS_23CartesianKernelFunctors11Compare_x_3INS_16Simple_cartesianINS_4GmpqEEEEENS2_INS3_INS_11Interval_ntILb0EEEEEEENS_15Exact_converterINS_5EpeckES5_EENS_16Approx_converterISC_S9_EELb1EEclINS_7Point_3ISC_EESJ_EENS_4SignERKT_RKT0_+0x20) [0x7f4e811aab60]
[zhouyi:07222] [ 2] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12Smaller_thanIS4_NS_6ObjectENS_8internal22In_place_list_iteratorINS_20SNC_in_place_list_smINS_14SNC_sphere_mapIS4_S5_bEEEESaISH_EEEiEclERKSB_SM_+0xab) [0x7f4e8120f90b]
[zhouyi:07222] [ 3] /usr/lib/libdolfin.so.1.2(_ZSt13__introselectIN9__gnu_cxx17__normal_iteratorIPN4CGAL6ObjectESt6vectorIS3_SaIS3_EEEElNS2_7K3_treeINS2_18SNC_k3_tree_traitsINS2_13SNC_decoratorINS2_13SNC_structureINS2_5EpeckENS2_17SNC_indexed_itemsEbEEEEEEE12Smaller_thanISD_S3_NS2_8internal22In_place_list_iteratorINS2_20SNC_in_place_list_smINS2_14SNC_sphere_mapISD_SE_bEEEESaISP_EEEiEEEvT_ST_ST_T0_T1_+0xde) [0x7f4e81213bce]
[zhouyi:07222] [ 4] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE25construct_splitting_planeIiEENS_7Plane_3IS4_EEN9__gnu_cxx17__normal_iteratorIPNS_6ObjectESt6vectorISF_SaISF_EEEESK_RSK_T_+0x7b) [0x7f4e81213d9b]
[zhouyi:07222] [ 5] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x89) [0x7f4e81214d49]
[zhouyi:07222] [ 6] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x8bd) [0x7f4e8121557d]
[zhouyi:07222] [ 7] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x887) [0x7f4e81215547]
[zhouyi:07222] [ 8] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x8bd) [0x7f4e8121557d]
[zhouyi:07222] [ 9] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x887) [0x7f4e81215547]
[zhouyi:07222] [10] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x8bd) [0x7f4e8121557d]
[zhouyi:07222] [11] /usr/lib/libdolfin.so.1.2(_ZN4CGAL7K3_treeINS_18SNC_k3_tree_traitsINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEEEE12build_kdtreeIiEEPNS9_4NodeERSt6vectorINS_6ObjectESaISE_EEN9__gnu_cxx17__normal_iteratorIPSE_SG_EET_SC_i+0x887) [0x7f4e81215547]
[zhouyi:07222] [12] /usr/lib/libdolfin.so.1.2(_ZN4CGAL40SNC_point_locator_by_spatial_subdivisionINS_13SNC_decoratorINS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEEEE10initializeEPS5_+0x3e6) [0x7f4e81215b46]
[zhouyi:07222] [13] /usr/lib/libdolfin.so.1.2(_ZN4CGAL27SNC_external_structure_baseIiNS_13SNC_structureINS_5EpeckENS_17SNC_indexed_itemsEbEEE14create_volumesEv+0x38a) [0x7f4e811dca4a]
[zhouyi:07222] [14] /usr/lib/libdolfin.so.1.2(_ZN4CGAL22SNC_external_structureINS_17SNC_indexed_itemsENS_13SNC_structureINS_5EpeckES1_bEEE24build_external_structureEv+0x1e8) [0x7f4e811dd558]
[zhouyi:07222] [15] /usr/lib/libdolfin.so.1.2(_ZN4CGAL16Nef_polyhedron_3INS_5EpeckENS_17SNC_indexed_itemsEbEC1IS1_NS_18Polyhedron_items_3ENS_18HalfedgeDS_defaultESaIiEEERNS_12Polyhedron_3IT_T0_T1_T2_EE+0x1ad) [0x7f4e8120027d]
[zhouyi:07222] [16] /usr/lib/libdolfin.so.1.2(+0x4f3512) [0x7f4e8117b512]
[zhouyi:07222] [17] /usr/lib/libdolfin.so.1.2(+0x4f3625) [0x7f4e8117b625]
[zhouyi:07222] [18] /usr/lib/libdolfin.so.1.2(+0x4f31bc) [0x7f4e8117b1bc]
[zhouyi:07222] [19] /usr/lib/libdolfin.so.1.2(_ZN6dolfin23GeometryToCGALConverter7convertERKNS_11CSGGeometryERN4CGAL12Polyhedron_3INS4_5EpickENS4_6Mesh_321Mesh_polyhedron_itemsIiEENS4_18HalfedgeDS_defaultESaIiEEEb+0xd6) [0x7f4e8117c046]
[zhouyi:07222] [20] /usr/lib/libdolfin.so.1.2(+0x8bde34) [0x7f4e81545e34]
[zhouyi:07222] [21] /usr/lib/libdolfin.so.1.2(_ZN6dolfin23VTKPlottableCSGGeometryC2EN5boost10shared_ptrIKNS_11CSGGeometryEEE+0x19) [0x7f4e81546099]
[zhouyi:07222] [22] /usr/lib/libdolfin.so.1.2(_ZN6dolfin18CreateVTKPlottableEN5boost10shared_ptrIKNS_11CSGGeometryEEE+0x37) [0x7f4e81546177]
[zhouyi:07222] [23] /usr/lib/libdolfin.so.1.2(_ZN6dolfin18CreateVTKPlottableEN5boost10shared_ptrIKNS_8VariableEEE+0x67) [0x7f4e81536587]
[zhouyi:07222] [24] /usr/lib/libdolfin.so.1.2(_ZN6dolfin10VTKPlotterC2EN5boost10shared_ptrIKNS_8VariableEEEP10QVTKWidget+0x55) [0x7f4e81539195]
[zhouyi:07222] [25] /usr/lib/libdolfin.so.1.2(_Z11get_plotterN5boost10shared_ptrIKN6dolfin8VariableEEESs+0x215) [0x7f4e815429e5]
[zhouyi:07222] [26] /usr/lib/libdolfin.so.1.2(_Z11plot_objectN5boost10shared_ptrIKN6dolfin8VariableEEENS0_IKNS1_10ParametersEEESs+0xb6) [0x7f4e81542db6]
[zhouyi:07222] [27] /usr/lib/libdolfin.so.1.2(_ZN6dolfin4plotEN5boost10shared_ptrIKNS_8VariableEEENS1_IKNS_10ParametersEEE+0x71) [0x7f4e815434b1]
[zhouyi:07222] [28] /usr/lib/python2.7/dist-packages/dolfin/cpp/_io.so(+0x2bd4e) [0x7f4e62ab4d4e]
[zhouyi:07222] [29] /usr/lib/python2.7/dist-packages/dolfin/cpp/_io.so(+0x37295) [0x7f4e62ac0295]
[zhouyi:07222] *** End of error message ***
Segmentation fault (core dumped)

Can somebody help?

asked Nov 14, 2013 by kickccat FEniCS Novice (200 points)

it seems it works in my mac with fenics 1.2.

commented Nov 14, 2013 by jying FEniCS User (2,020 points)

1 Answer

+1 vote

This is due to a STL bug in Ubuntu 13.10. See https://bugs.launchpad.net/bugs/1246802. A fix is on the way from Ubuntu. See https://bugs.launchpad.net/ubuntu/+source/gcc-4.8/+bug/1246802/comments/32 is you want to fix it now.

answered Nov 15, 2013 by Garth N. Wells FEniCS Expert (35,930 points)

Hi,
I patched the package “gcc-4.8” 4.8.1-10ubuntu9, but still failed and got the same error information.

commented Nov 18, 2013 by kickccat FEniCS Novice (200 points)

Segfault also for me, used to run ok with older Ubuntu, code snippet at bottom of mail.

Ubuntu 13.10-desktop-amd64, running in VMWare Player 6.0.1 under Windows 8.
32 MB Ram
4 Cores
Fenics 1.2
Recommended update installed: “gcc-4.8” 4.8.1-10ubuntu9

Going back to Ubuntu-12.10-desktop-i386 (all other unchanged) solves the problem.

Kind regards
Jacques de Hooge
Netherlands

BEGIN code snippet

dirichletBoundaryConditions = [DirichletBC (functionSpace, HeartPotentialExpression (), facetMeshFunction, uniqueSourceFacetLabel)]

leftHandSide = sigma * inner (grad (trialFunction), grad (testFunction)) * dx
rightHandSide = Constant (0) * testFunction * dx

A, b = assemble_system (leftHandSide, rightHandSide, dirichletBoundaryConditions, keep_diagonal = True)

solve (A, potential.vector (), b,'gmres', 'default')

END code snippet

commented Nov 21, 2013 by jacdeh FEniCS Novice (120 points)

Okay, anyway thanks. I found 13.10 is not so stable and return to the precise, then solved the problem.

commented Nov 21, 2013 by kickccat FEniCS Novice (200 points)
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