Jan, Thanks for all your suggestions. For future reference I'd like to give an update on solving the issue. The code in BoundingBoxTree3D.h that segfaults is called through std::nth_element function, so I guess that using GCC 4.8.2 my FEniCS installation was susceptible to this bug of the standard library https://gcc.gnu.org/bugzilla/show_bug.cgi?id=58800
I recompiled everything (with some extra efforts) with GCC 5.2 and the problem disappeared. Thanks very much for the hints! Best, Paolo On Mon, Oct 26, 2015 at 12:57 PM, Jan Blechta <[email protected]> wrote: > On Mon, 26 Oct 2015 10:56:43 -0400 > Paolo Di Achille <[email protected]> wrote: > > > Jan, > > > > Thanks very much for looking into this. The output for your code is > > 4294967295 > > This is 32-bit uint. Are you sure you've compiled the code with the same > compiler and C/C++ headers as DOLFIN is compiled with? > > > > > And sorry for the broken link, the following should work instead > > https://yale.box.com/s/j20x0loaclio1wsjzonv7khhf3iov2lg > > For this mesh, the value of mesh.num_entities(3) is 888780. > > I cannot reproduce the problem with the mesh. You may try digging more > deeply into the problem using debugger. > > Jan > > > > > Best, > > Paolo > > > > On Mon, Oct 26, 2015 at 9:50 AM, Jan Blechta > > <[email protected]> wrote: > > > > > The link to the meshfile does not work. Can you provide a mesh > > > again? > > > > > > There's a conversion from size_t to uint in [1], which could > > > overflow if you have 16-bit uint. What's the output of > > > //---------------------------------------------------- > > > echo "#include <limits> > > > #include <iostream> > > > > > > int main() { > > > std::cout << std::numeric_limits<unsigned int>::max() << > > > std::endl; > > > > > > return 0; > > > } > > > " | c++ -std=c++11 -xc++ - && ./a.out > > > //---------------------------------------------------- > > > > > > [1] > > > > > > > https://bitbucket.org/fenics-project/dolfin/src/8ad7544e62714eaf561e52880925d3713756f3c0/dolfin/geometry/GenericBoundingBoxTree.cpp?at=master&fileviewer=file-view-default#GenericBoundingBoxTree.cpp-93 > > > > > > Jan > > > > > > > > > On Sat, 24 Oct 2015 20:13:41 -0400 > > > Paolo Di Achille <[email protected]> wrote: > > > > > > > Jan, > > > > > > > > Thanks very much for the suggestions. I used the debugger using > > > > your instructions and below you can find the first five frames of > > > > the backtrace > > > > > > > > #0 0x00002aaabb908d34 in > > > > dolfin::BoundingBoxTree3D::less_z_bbox::operator()(unsigned int, > > > > unsigned int) () > > > > at > > > /home/fas/pd/src/dolfin-1.6.0/dolfin/geometry/BoundingBoxTree3D.h:76 > > > > > > > > #1 0x00002aaabb90f38a in __gnu_cxx::__normal_iterator<unsigned > > > > int*, std::vector<unsigned int, std::allocator<unsigned int> > > > > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator<unsigned > > > > int*, std::vector<unsigned int, std::allocator<unsigned int> > >, > > > > unsigned int, > > > > > > > > dolfin::BoundingBoxTree3D::less_z_bbox>(__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> > >, unsigned int const&, > > > > dolfin::BoundingBoxTree3D::less_z_bbox) () > > > > at > /gpfs/apps/hpc/Langs/GCC/4.8.2/include/c++/4.8.2/bits/stl_algo.h:2263 > > > > > > > > #2 0x00002aaabb90c89d in __gnu_cxx::__normal_iterator<unsigned > > > > int*, std::vector<unsigned int, std::allocator<unsigned int> > > > > > > > std::__unguarded_partition_pivot<__gnu_cxx::__normal_iterator<unsigned > > > > int*, std::vector<unsigned int, std::allocator<unsigned int> > >, > > > > > > > > dolfin::BoundingBoxTree3D::less_z_bbox>(__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::BoundingBoxTree3D::less_z_bbox) () > > > > at > /gpfs/apps/hpc/Langs/GCC/4.8.2/include/c++/4.8.2/bits/stl_algo.h:2296 > > > > > > > > #3 0x00002aaabb90afc8 in void > > > > std::__introselect<__gnu_cxx::__normal_iterator<unsigned int*, > > > > std::vector<unsigned int, std::allocator<unsigned int> > >, long, > > > > > > > > dolfin::BoundingBoxTree3D::less_z_bbox>(__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> > >, > > > > __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned > > > > int, std::allocator<unsigned int> > >, long, > > > > dolfin::BoundingBoxTree3D::less_z_bbox) () > > > > at > /gpfs/apps/hpc/Langs/GCC/4.8.2/include/c++/4.8.2/bits/stl_algo.h:2394 > > > > > > > > #4 0x00002aaabb90a326 in void > > > > std::nth_element<__gnu_cxx::__normal_iterator<unsigned int*, > > > > std::vector<unsigned int, std::allocator<unsigned int> > >, > > > > > > > > dolfin::BoundingBoxTree3D::less_z_bbox>(__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> > >, > > > > __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned > > > > int, std::allocator<unsigned int> > >, > > > > dolfin::BoundingBoxTree3D::less_z_bbox) () > > > > at > /gpfs/apps/hpc/Langs/GCC/4.8.2/include/c++/4.8.2/bits/stl_algo.h:5417 > > > > > > > > #5 0x00002aaabb909bb2 in > > > > dolfin::BoundingBoxTree3D::sort_bboxes(unsigned long, > > > > std::vector<double, std::allocator<double> > const&, > > > > __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned > > > > int, std::allocator<unsigned int> > > const&, > > > > __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned > > > > int, std::allocator<unsigned int> > > const&, > > > > __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned > > > > int, std::allocator<unsigned int> > > const&) () > > > > at > /home/fas/pd/src/dolfin-1.6.0/dolfin/geometry/BoundingBoxTree3D.h:249 > > > > > > > > The segfault seems to arise at line 76 as reported below, inside > > > > struct less_z_bbox of BoundingBoxTree3D.h > > > > > > > > | 72 inline bool operator()(unsigned int i, unsigned > > > > int j) > > > > > > > > | 73 > > > > { > > > > > > > > | 74 const double* bi = bboxes.data() + > > > > 6*i; > > > > > > > > | 75 const double* bj = bboxes.data() + > > > > 6*j; > > > > > > > > | 76 return bi[2] + bi[5] < bj[2] + > > > > bj[5]; > > > > > > > > | 77 } > > > > > > > > when the integer 'i' gets a much larger value than it gets in > > > > many previous successful calls. Also, I was not able to reproduce > > > > the segmentation fault with smaller mesh files, but the error > > > > consistently occurs for relatively large meshes (~500 000 > > > > elements), like the one I uploaded at this link: > > > > > > > > https://yale.box.com/s/yyls3w8j2j7refryywy9yj79pvalhjyd > > > > > > > > Please let me know if I can any provide further information, and > > > > again thanks very much! > > > > > > > > Best, > > > > Paolo > > > > > > > > > > > > > > > > > > > > On Sat, Oct 24, 2015 at 12:49 PM, Jan Blechta > > > > <[email protected]> wrote: > > > > > > > > > You can try debugger > > > > > > > > > > gdb -ex r -args python script.py > > > > > <program terminates with segfault> > > > > > (GDB) bt > > > > > <stack trace> > > > > > (GDB) f <suspicious_frame> > > > > > (GDB) w > > > > > <code in question> > > > > > (GDB) p <suspicious_pointer> > > > > > > > > > > Can you also provide us the mesh? > > > > > > > > > > Jan > > > > > > > > > > > > > > > On Sat, 24 Oct 2015 11:24:23 -0400 > > > > > Paolo Di Achille <[email protected]> wrote: > > > > > > > > > > > Dear FEniCS users and developers, > > > > > > > > > > > > I don't seem to be able to build the BoundingBoxTree of a > > > > > > correctly loaded mesh using a recent installation from source > > > > > > of FEniCS 1.6.0 on a local cluster. The following minimal code > > > > > > results in a segfault error > > > > > > > > > > > > >>> from dolfin import * > > > > > > >>> mm = Mesh('mesh.xml') > > > > > > >>> mm.bounding_box_tree().build(mm) > > > > > > > > > > > > Surprisingly, I can use with no apparent issues other features > > > > > > that do not explicitly require building a tree (e.g. solving a > > > > > > problem in parallel, I/O of XDMF files), but the software > > > > > > fails, probably for the same reason, when I need to evaluate > > > > > > a function at a point of given coordinates. Likely, I must > > > > > > have missed some installation requirements and any pointers > > > > > > or suggestions would be highly appreciated. > > > > > > > > > > > > My current installation of FEniCS was built against > > > > > > OpenMPI-1.8.1, Python-2.7.6, Swig-3.0.7, Boost-1.59.0, > > > > > > HDF5-1.8.10, VTK-5.10.1, Scotch-6.0.4, Petsc-3.6.2 using > > > > > > GCC-4.8.2 and Cmake-3.3.2. Also no error was output during > > > > > > compilation and linking. > > > > > > > > > > > > Thanks very much! Best, > > > > > > Paolo > > > > > > > > > > > > > > > > > >
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