If this segfault is easy to reproduce I can try it here, if you send a script. I have gt 2.12 python 2.7.11 gcc 4.9.3 boost 1.59.0.
On Thu, Jan 28, 2016 at 11:44 PM, Eric <[email protected]> wrote: > Hi, > > I have a segmentation fault create with a specific data set (other data set > works). > I have some difficulty to find the origin. I try to create a small example, > but for the moment I can only give you the output and backtrack of gdb: > > *Output:* > Program received signal SIGSEGV, Segmentation fault. > 0x00007ffff0473d62 in uw_init_context_1 () from > /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 > Missing separate debuginfos, use: debuginfo-install > atlas-3.8.4-2.el6.x86_64 > boost-iostreams-1.41.0-27.el6.x86_64 boost-python-1.41.0-27.el6.x86_64 > boost-regex-1.41.0-27.el6.x86_64 boost-system-1.41.0-27.el6.x86_64 > boost-thread-1.41.0-27.el6.x86_64 bzip2-libs-1.0.5-7.el6_0.x86_64 > fontconfig-2.8.0-5.el6.x86_64 freetype-2.3.11-15.el6_6.1.x86_64 > glibc-2.12-1.166.el6.x86_64 keyutils-libs-1.4-5.el6.x86_64 > krb5-libs-1.10.3-42.el6.x86_64 libX11-1.6.0-6.el6.x86_64 > libXau-1.0.6-4.el6.x86_64 libXext-1.3.2-2.1.el6.x86_64 > libXrender-0.9.8-2.1.el6.x86_64 libcom_err-1.41.12-22.el6.x86_64 > libicu-4.2.1-12.el6.x86_64 libjpeg-turbo-1.2.1-3.el6_5.x86_64 > libpng-1.2.49-2.el6_7.x86_64 libselinux-2.0.94-5.8.el6.x86_64 > libtiff-3.9.4-10.el6_5.x86_64 libxcb-1.9.1-3.el6.x86_64 > openssl-1.0.1e-42.el6_7.2.x86_64 pango-1.28.1-10.el6.x86_64 > python-libs-2.6.6-64.el6.x86_64 sqlite-3.6.20-1.el6_7.2.x86_64 > zlib-1.2.3-29.el6.x86_64 > > *bt*: > #0 0x00007ffff0473d62 in uw_init_context_1 () from > /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 > #1 0x00007ffff047420e in _Unwind_RaiseException () from > /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 > #2 0x00007ffff06d833b in __cxa_throw () at > ../../../../libstdc++-v3/libsupc++/eh_throw.cc:82 > #3 0x00007fffe4ae40f3 in > > _ZNK10graph_tool6detail12graph_actionISt5_BindIFNS_14add_new_vertexESt12_PlaceholderILi1EESt17reference_wrapperINS_14GraphInterfaceEEmS6_IN5boost6python3api6objectEEEENS0_15all_graph_viewsEN4mpl_5bool_ILb0EEEJEEclIJEEEvDpOT_ > () from > /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #4 0x00007fffe4a51dee in > graph_tool::add_vertex(graph_tool::GraphInterface&, unsigned long) () from > /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #5 0x00007fffe4a92bfe in > > boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::api::object > (*)(graph_tool::GraphInterface&, unsigned long), > boost::python::default_call_policies, > boost::mpl::vector3<boost::python::api::object, > graph_tool::GraphInterface&, unsigned long> > >::operator()(_object*, > _object*) () from > /***********/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #6 0x00007fffe303ca86 in boost::python::objects::function::call(_object*, > _object*) const () from /usr/lib64/libboost_python.so.5 > #7 0x00007fffe303cd98 in ?? () from /usr/lib64/libboost_python.so.5 > #8 0x00007fffe30452a3 in > boost::python::detail::exception_handler::operator()(boost::function0<void> > const&) const () from /usr/lib64/libboost_python.so.5 > #9 0x00007fffe3ea37a3 in > boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, > boost::python::detail::translate_exception<graph_tool::ValueException, > void (*)(graph_tool::ValueException const&)>, > boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void > (*)(graph_tool::ValueException const&)> > >, bool, > boost::python::detail::exception_handler const&, boost::function0<void> > const&>::invoke(boost::detail::function::function_buffer&, > boost::python::detail::exception_handler const&, boost::function0<void> > const&) () from > /********/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #10 0x00007fffe304527d in > boost::python::detail::exception_handler::operator()(boost::function0<void> > const&) const () from /usr/lib64/libboost_python.so.5 > #11 0x00007fffe3ea36d3 in > boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, > boost::python::detail::translate_exception<graph_tool::IOException, void > (*)(graph_tool::IOException const&)>, > boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void > (*)(graph_tool::IOException const&)> > >, bool, > boost::python::detail::exception_handler const&, boost::function0<void> > const&>::invoke(boost::detail::function::function_buffer&, > boost::python::detail::exception_handler const&, boost::function0<void> > const&) () from > /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #12 0x00007fffe304527d in > boost::python::detail::exception_handler::operator()(boost::function0<void> > const&) const () from /usr/lib64/libboost_python.so.5 > #13 0x00007fffe3ea3603 in > boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, > boost::python::detail::translate_exception<graph_tool::GraphException, > void (*)(graph_tool::GraphException const&)>, > boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void > (*)(graph_tool::GraphException const&)> > >, bool, > boost::python::detail::exception_handler const&, boost::function0<void> > const&>::invoke(boost::detail::function::function_buffer&, > boost::python::detail::exception_handler const&, boost::function0<void> > const&) () from > /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > #14 0x00007fffe3045063 in > boost::python::handle_exception_impl(boost::function0<void>) () from > /usr/lib64/libboost_python.so.5 > #15 0x00007fffe303a928 in ?? () from /usr/lib64/libboost_python.so.5 > #16 0x00000000004197c7 in PyObject_Call (func=0x1c0f070, arg=<value > optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 > #17 0x00000000004a80b0 in do_call (f=<value optimized out>, > throwflag=<value > optimized out>) at Python/ceval.c:4239 > #18 call_function (f=<value optimized out>, throwflag=<value optimized > out>) > at Python/ceval.c:4044 > #19 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized > out>) at Python/ceval.c:2666 > #20 0x00000000004aa627 in PyEval_EvalCodeEx (co=0x10b66b0, globals=<value > optimized out>, locals=<value optimized out>, args=<value optimized out>, > argcount=1, kws=0x44c8a56c8, kwcount=0, defs=0x1bf7b28, defcount=1, > closure=0x0) at Python/ceval.c:3253 > #21 0x00000000004a87d4 in fast_function (f=<value optimized out>, > throwflag=<value optimized out>) at Python/ceval.c:4117 > #22 call_function (f=<value optimized out>, throwflag=<value optimized > out>) > at Python/ceval.c:4042 > #23 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized > out>) at Python/ceval.c:2666 > . > . (loop) > . > #124095 0x00000000004a9ab5 in fast_function (f=<value optimized out>, > throwflag=<value optimized out>) at Python/ceval.c:4107 > #124096 call_function (f=<value optimized out>, throwflag=<value optimized > out>) at Python/ceval.c:4042 > #124097 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value > optimized out>) at Python/ceval.c:2666 > #124098 0x00000000004aa627 in PyEval_EvalCodeEx (co=0x7ffff7ece530, > globals=<value optimized out>, locals=<value optimized out>, args=<value > optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, > closure=0x0) > at Python/ceval.c:3253 > #124099 0x00000000004aa732 in PyEval_EvalCode (co=<value optimized out>, > globals=<value optimized out>, locals=<value optimized out>) at > Python/ceval.c:667 > ---Type <return> to continue, or q <return> to quit--- > #124100 0x00000000004cad5e in run_mod (fp=0x8f3600, filename=0x7fffffffdc71 > "/*****/nektar_graph.py", start=<value optimized out>, globals=0x7fe690, > locals=0x7fe690, closeit=1, flags=0x7fffffffd760) > at Python/pythonrun.c:1370 > #124101 PyRun_FileExFlags (fp=0x8f3600, filename=0x7fffffffdc71 > "/*******/nektar_graph.py", start=<value optimized out>, globals=0x7fe690, > locals=0x7fe690, closeit=1, flags=0x7fffffffd760) > at Python/pythonrun.c:1356 > #124102 0x00000000004caf87 in PyRun_SimpleFileExFlags (fp=0x8f3600, > filename=0x7fffffffdc71 "/*********/nektar_graph.py", closeit=1, > flags=0x7fffffffd760) at Python/pythonrun.c:948 > #124103 0x0000000000414e72 in Py_Main (argc=<value optimized out>, > argv=<value optimized out>) at Modules/main.c:640 > #124104 0x000000339ee1ed5d in __libc_start_main () from /lib64/libc.so.6 > > > I use the last version of graph-tool(2.12), with python-2.7.6, gcc-4.9.3, > boost-1.59.0. > Should I try with python-3.X ? > > It will be useful, if you have any advice or information to found the > origin > of this segmentation fault. Without I comeback when I have more > information. > > Regards, > Eric. > > > > -- > View this message in context: > http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Segmentation-fault-when-I-try-to-access-to-a-vertex-tp4026392.html > Sent from the Main discussion list for the graph-tool project mailing list > archive at Nabble.com. > _______________________________________________ > graph-tool mailing list > [email protected] > http://lists.skewed.de/mailman/listinfo/graph-tool >
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