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.
--
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