Segmentation fault in BoundingBoxTree2D

Issue #156 invalid

Nico Schlömer created an issue 2013-11-21

Dolfin (from git/master) segfaults in both interpolate() and project() onto a submesh. I was not able to reproduce the issue with standard submeshes (e.g., from http://fenicsproject.org/documentation/dolfin/dev/python/demo/pde/subdomains-poisson/python/documentation.html) which I why I'm also attaching the domain data.

The code for reproducing the issue is

from dolfin import *

mesh = Mesh('mydomain.xml')
domains = MeshFunction('size_t', mesh, 'mydomain_physical_region.xml')

V = FunctionSpace(mesh, 'CG', 1)

expr = Expression('x[0]')
u = project(expr, V)

submesh = SubMesh(mesh, domains, 1)
V_submesh = FunctionSpace(submesh, 'CG', 1)

# Segfault:
u_submesh = project(u, V_submesh)

# Segfault:
#u_submesh = Function(V_submesh)
#u_submesh.interpolate(u)

Comments (13)

Jan Blechta
@nschloe Can't reproduce. Can you back-trace it using debugger?
- 2013-11-22T13:55:14+00:00
Nico Schlömer reporter
Note that the segfault doesn't occur with 1.2.0. I'll post a backtrace later.
- 2013-11-22T14:12:55+00:00

Nico Schlömer reporter

Backtraces:

(gdb) run main.py
Starting program: /usr/bin/python main.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Solving linear system of size 8457 x 8457 (PETSc Krylov solver).

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff165647c in dolfin::BoundingBoxTree2D::less_y::operator() (this=0x7fffffffb0a0, 
    i=4156255928, j=13639)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/BoundingBoxTree2D.h:65
65          return bi[1] + bi[3] < bj[1] + bj[3];

(gdb) backtrace
#0  0x00007ffff165647c in dolfin::BoundingBoxTree2D::less_y::operator() (this=0x7fffffffb0a0, 
    i=4156255928, j=13639)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/BoundingBoxTree2D.h:65
#1  0x00007ffff165ed3c in std::__unguarded_partition<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > >, unsigned int, dolfin::BoundingBoxTree2D::less_y> (__first=..., __last=..., __pivot=@0x1fd6c50: 13639, __comp=...)
    at /usr/include/c++/4.8/bits/stl_algo.h:2263
#2  0x00007ffff165c788 in std::__unguarded_partition_pivot<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > >, dolfin::BoundingBoxTree2D::less_y> (__first=..., __last=..., __comp=...) at /usr/include/c++/4.8/bits/stl_algo.h:2296
#3  0x00007ffff165ab73 in std::__introselect<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > >, long, dolfin::BoundingBoxTree2D::less_y>
    (__first=..., __nth=..., __last=..., __depth_limit=3, __comp=...)
    at /usr/include/c++/4.8/bits/stl_algo.h:2394
#4  0x00007ffff16594a7 in std::nth_element<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > >, dolfin::BoundingBoxTree2D::less_y> (
    __first=..., __nth=..., __last=..., __comp=...)
    at /usr/include/c++/4.8/bits/stl_algo.h:5417
#5  0x00007ffff16583d3 in boost::range::nth_element<std::pair<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > >, __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > >, dolfin::BoundingBoxTree2D::less_y> (rng=..., nth=..., sort_pred=...)
    at /usr/include/boost/range/algorithm/nth_element.hpp:66
#6  0x00007ffff1656eeb in dolfin::BoundingBoxTree2D::sort_bboxes (this=0x1ef0250, axis=1, 
    leaf_bboxes=..., begin=..., middle=..., end=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/BoundingBoxTree2D.h:211
#7  0x00007ffff1653572 in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:308
#8  0x00007ffff165359d in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:311
#9  0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#10 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#11 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#12 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#13 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.c---Type <return> to continue, or q <return> to quit---
pp:312
#14 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#15 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#16 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#17 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#18 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#19 0x00007ffff16535cb in dolfin::GenericBoundingBoxTree::_build (this=0x1ef0250, 
    leaf_bboxes=..., begin=..., end=..., gdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:312
#20 0x00007ffff1651de9 in dolfin::GenericBoundingBoxTree::build (this=0x1ef0250, mesh=..., 
    tdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/GenericBoundingBoxTree.cpp:78
#21 0x00007ffff1663b49 in dolfin::BoundingBoxTree::build (this=0x1b82440, mesh=..., tdim=2)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/BoundingBoxTree.cpp:71
#22 0x00007ffff1663864 in dolfin::BoundingBoxTree::build (this=0x1b82440, mesh=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/geometry/BoundingBoxTree.cpp:45
#23 0x00007ffff18cf774 in dolfin::Mesh::bounding_box_tree (this=0x1d7f4d0)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/mesh/Mesh.cpp:401
#24 0x00007ffff18401b3 in dolfin::Function::non_matching_eval (this=0x1b647b0, values=..., 
    x=..., ufc_cell=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/function/Function.cpp:514
#25 0x00007ffff183fd30 in dolfin::Function::eval (this=0x1b647b0, values=..., x=..., 
    ufc_cell=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/function/Function.cpp:494
#26 0x00007ffff184fff2 in dolfin::GenericFunction::evaluate (this=0x1b647b0, 
    values=0x7fffffffc470, coordinates=0x7fffffffc480, cell=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/function/GenericFunction.cpp:185
#27 0x00007fffd3d702f6 in ffc_form_06236707c63ae02ee345885e87278c5e7db8edcb_finite_element_0::evaluate_dofs(double*, ufc::function const&, double const*, int, ufc::cell const&) const ()
   from /home/nschloe/.instant/cache/ffc_form_06236707c63ae02ee345885e87278c5e7db8edcb/_ffc_form_06236707c63ae02ee345885e87278c5e7db8edcb.so
#28 0x00007ffff185044e in dolfin::FiniteElement::evaluate_dofs (this=0x1b9b240, 
    values=0x169bc00, f=..., vertex_coordinates=0x1b86f00, cell_orientation=0, c=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/fem/FiniteElement.h:232
#29 0x00007ffff1850246 in dolfin::GenericFunction::restrict_as_ufc_function (this=0x1b647b0, 
    w=0x169bc00, element=..., dolfin_cell=..., ufc_cell=...)
---Type <return> to continue, or q <return> to quit---
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/function/GenericFunction.cpp:201
#30 0x00007ffff1840e14 in dolfin::Function::restrict(double*, dolfin::FiniteElement const&, dolfin::Cell const&, ufc::cell const&) const (this=0x1b647b0, w=0x169bc00, element=..., 
    dolfin_cell=..., ufc_cell=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/function/Function.cpp:593
#31 0x00007ffff16cfd02 in dolfin::UFC::update (this=0x7fffffffd1b0, c=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/fem/UFC.cpp:139
#32 0x00007ffff16e2938 in dolfin::SystemAssembler::cell_wise_assembly (tensors=..., ufc=..., 
    data=..., boundary_values=..., cell_domains=0x0, exterior_facet_domains=0x0)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/fem/SystemAssembler.cpp:415
#33 0x00007ffff16e13d1 in dolfin::SystemAssembler::assemble (this=0x1baa430, A=0x1ef03f0, 
    b=0x1ba2330, x0=0x0)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/fem/SystemAssembler.cpp:294
#34 0x00007ffff16dfac9 in dolfin::SystemAssembler::assemble (this=0x1baa430, A=..., b=...)
    at /home/nschloe/software/fenics/dolfin/dev/source/dolfin/fem/SystemAssembler.cpp:110
#35 0x00007fffd7a4c812 in _wrap_SystemAssembler_assemble__SWIG_0 (nobjs=3, 
    swig_obj=0x7fffffffd5f0)
    at /home/nschloe/software/fenics/dolfin/dev/build/dolfin/swig/modules/fem/modulePYTHON_wrap.cxx:27469
#36 0x00007fffd7a4d6fa in _wrap_SystemAssembler_assemble (self=0x0, args=0x17f7730)
    at /home/nschloe/software/fenics/dolfin/dev/build/dolfin/swig/modules/fem/modulePYTHON_wrap.cxx:27784
#37 0x000000000053473a in PyEval_EvalFrameEx ()
#38 0x0000000000505b24 in PyEval_EvalCodeEx ()
#39 0x000000000052e237 in PyEval_EvalFrameEx ()
#40 0x0000000000505b24 in PyEval_EvalCodeEx ()
#41 0x000000000052e237 in PyEval_EvalFrameEx ()
#42 0x0000000000567cdc in PyEval_EvalCode ()
#43 0x0000000000451adb in ?? ()
#44 0x0000000000451e5b in PyRun_FileExFlags ()
#45 0x0000000000452394 in PyRun_SimpleFileExFlags ()
#46 0x0000000000453ead in Py_Main ()
#47 0x00007ffff7816de5 in __libc_start_main (main=0x453f6b <main>, argc=2, 
    ubp_av=0x7fffffffdf28, init=<optimized out>, fini=<optimized out>, 
    rtld_fini=<optimized out>, stack_end=0x7fffffffdf18) at libc-start.c:260
#48 0x00000000005786be in _start ()

-- Looks like an uninitialized argunment i in dolfin/geometry/BoundingBoxTree2D.h:65.

2013-11-22T16:22:35+00:00

Nico Schlömer reporter
- changed title to Segmentation fault in BoundingBoxTree2D
- 2013-11-22T19:32:53+00:00
Jan Blechta
@nschloe Do you have Ubuntu 13.10? If yes, you should read FEniCS mailing-list. http://fenicsproject.org/pipermail/fenics/2013-November/000743.html :-P

Fix is available, see https://bugs.launchpad.net/ubuntu/+source/gcc-4.8/+bug/1246802/comments/32

Please, mark the issue as invalid.
- 2013-11-22T22:21:24+00:00
Nico Schlömer reporter
I'm indeed running Ubuntu 13.10, but I'm not sure if this is the fix. On dev, instead of std::nth_element, boost:nth_element is used (at least on my computer).
- 2013-11-24T18:17:40+00:00
Jan Blechta
@nschloe Check frame 4 in your backtrace - there is std::nth_element call.

Do you have the newest DOLFIN? @logg fixed another related bug.
- 2013-11-24T19:55:19+00:00
Nico Schlömer reporter
- changed status to invalid
You're right; there's both boost:nth_element and std::nth_element present. Is the one calling the other? Anyhow, upgrading to 4.8.1-10ubuntu9 fixes the issue for me.
- 2013-11-25T10:29:33+00:00
Anders Logg (Chalmers)
There shouldn't be any call to std::nth_element anywhere in the code. All of them have been replaced with boost::nth_element (I hope).
- 2013-11-25T13:41:31+00:00

Jan Blechta

@logg It does not seem so

r0:~/fenics/fenics-work/src/dolfin/dolfin>grep -iIHr "std::nth_element" *
geometry/GenericBoundingBoxTree.cpp:    std::nth_element(begin, middle, end, less_x_point(points));
geometry/GenericBoundingBoxTree.cpp:    std::nth_element(begin, middle, end, less_y_point(points));
geometry/GenericBoundingBoxTree.cpp:    std::nth_element(begin, middle, end, less_z_point(points));
geometry/BoundingBoxTree2D.h:        std::nth_element(begin, middle, end, less_x(leaf_bboxes));
geometry/BoundingBoxTree2D.h:        std::nth_element(begin, middle, end, less_y(leaf_bboxes));
geometry/BoundingBoxTree3D.h:        std::nth_element(begin, middle, end, less_x_bbox(leaf_bboxes));
geometry/BoundingBoxTree3D.h:        std::nth_element(begin, middle, end, less_y_bbox(leaf_bboxes));
geometry/BoundingBoxTree3D.h:        std::nth_element(begin, middle, end, less_z_bbox(leaf_bboxes));
geometry/BoundingBoxTree1D.h:      std::nth_element(begin, middle, end, less_x(leaf_bboxes));
geometry/GenericBoundingBoxTree.h:// std::nth_element as a workaround for a bug in STL introduced in GCC

2013-11-25T14:52:47+00:00

Nico Schlömer reporter
@logg From the backtrace, it appears that boost::nth_element calls std::nth_element. This is confirmed by looking at Boost's source, http://www.boost.org/doc/libs/1_53_0/boost/range/algorithm/nth_element.hpp. Hence, I'm not sure what the purpose of the #ifdefing may be. Does it really work around the bug for you?
- 2013-11-25T17:12:03+00:00
Nico Schlömer reporter
@blechta I believe that all those explicit std::nth_element are #ifdefd out.
- 2013-11-25T19:05:35+00:00
Jan Blechta
@nschloe You're correct!
- 2013-11-26T02:31:23+00:00
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Assignee: –

Type: bug

Priority: major

Status: invalid

Component: –

Milestone: –

Version: dev

Votes: 1

Watchers: 4