Segmentation fault when I try to access to a vertex
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/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
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 <eric.audemard@umontreal.ca> 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/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. _______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
Thanks for your offer, but I can't reproduce this segmentation fault on small script/example. I let you know if I found a way. When I check libgraph_tool_core.so with ldd: linux-vdso.so.1 => (0x00007ffdd6d57000) libpython2.7.so.1.0 => /soft/bioinfo/linux_RH6/python-2.7.6/lib/libpython2.7.so.1.0 (0x00007ff7cbc49000) libboost_iostreams.so.5 => /usr/lib64/libboost_iostreams.so.5 (0x00007ff7cba10000) libboost_python.so.5 => /usr/lib64/libboost_python.so.5 (0x00007ff7cb7bf000) libboost_regex.so.5 => /usr/lib64/libboost_regex.so.5 (0x00007ff7cb4cb000) libboost_coroutine.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_coroutine.so.1.59.0 (0x00007ff7cb2be000) libCGAL.so.11 => /u/eaudemard/bin/lib/libCGAL.so.11 (0x00007ff7cb095000) libexpat.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/libexpat.so.1 (0x00007ff7cae6c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ff7cac5a000) libstdc++.so.6 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libstdc++.so.6 (0x00007ff7ca948000) libm.so.6 => /lib64/libm.so.6 (0x00007ff7ca6c4000) libc.so.6 => /lib64/libc.so.6 (0x00007ff7ca32f000) libgcc_s.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libgcc_s.so.1 (0x00007ff7ca119000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff7c9efc000) libdl.so.2 => /lib64/libdl.so.2 (0x00007ff7c9cf7000) libutil.so.1 => /lib64/libutil.so.1 (0x00007ff7c9af4000) libz.so.1 => /lib64/libz.so.1 (0x00007ff7c98de000) libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ff7c9537000) libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ff7c91e5000) libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ff7c8e4f000) libboost_context.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_context.so.1.59.0 (0x00007ff7c8c43000) libboost_thread.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_thread.so.1.59.0 (0x00007ff7c8a21000) libboost_chrono.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_chrono.so.1.59.0 (0x00007ff7c881b000) libboost_system.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_system.so.1.59.0 (0x00007ff7c8617000) librt.so.1 => /lib64/librt.so.1 (0x00007ff7c840f000) libmpfr.so.4 => /u/eaudemard/bin/lib/libmpfr.so.4 (0x00007ff7c81b0000) libgmp.so.10 => /u/eaudemard/bin/lib/libgmp.so.10 (0x00007ff7c7f39000) libboost_thread-mt.so.5 => /usr/lib64/libboost_thread-mt.so.5 (0x00007ff7c7d24000) libboost_system-mt.so.5 => /usr/lib64/libboost_system-mt.so.5 (0x00007ff7c7b21000) /lib64/ld-linux-x86-64.so.2 (0x0000003756800000) libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ff7c69d5000) Some libboost are linked with the good version of boost but some others are linked an oldest version (1.41). I try to fixe this with the option "--with-boost-python=" of configure but it doesn't work: ./configure --prefix=/u/eaudemard/bin/ --with-python-module-path=/u/eaudemard/bin/lib/python2.7/site-packages/ --with-boost=/soft/bioinfo/linux_RH6/boost-1.59.0/ --with-boost-libdir=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/ --with-boost-python=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 ... checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -l/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no checking for exit in -lboost_python-/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no checking for exit in -lboost_python... yes ls -l /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 -rwxr-xr-x. 1 adsoft users 404020 Oct 19 13:39 /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 After this i try apm -e of the old version and this time the configure don't find "boost_python" checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no configure: error: No usable boost::python found Have you an idea on that point ? Regards, Eric. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Could be this that cause the segfault. On Fri, Jan 29, 2016 at 7:21 PM, Eric <eric.audemard@umontreal.ca> wrote:
Thanks for your offer, but I can't reproduce this segmentation fault on small script/example. I let you know if I found a way.
When I check libgraph_tool_core.so with ldd: linux-vdso.so.1 => (0x00007ffdd6d57000) libpython2.7.so.1.0 => /soft/bioinfo/linux_RH6/python-2.7.6/lib/libpython2.7.so.1.0 (0x00007ff7cbc49000) libboost_iostreams.so.5 => /usr/lib64/libboost_iostreams.so.5 (0x00007ff7cba10000) libboost_python.so.5 => /usr/lib64/libboost_python.so.5 (0x00007ff7cb7bf000) libboost_regex.so.5 => /usr/lib64/libboost_regex.so.5 (0x00007ff7cb4cb000) libboost_coroutine.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_coroutine.so.1.59.0 (0x00007ff7cb2be000) libCGAL.so.11 => /u/eaudemard/bin/lib/libCGAL.so.11 (0x00007ff7cb095000) libexpat.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/libexpat.so.1 (0x00007ff7cae6c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ff7cac5a000) libstdc++.so.6 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libstdc++.so.6 (0x00007ff7ca948000) libm.so.6 => /lib64/libm.so.6 (0x00007ff7ca6c4000) libc.so.6 => /lib64/libc.so.6 (0x00007ff7ca32f000) libgcc_s.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libgcc_s.so.1 (0x00007ff7ca119000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff7c9efc000) libdl.so.2 => /lib64/libdl.so.2 (0x00007ff7c9cf7000) libutil.so.1 => /lib64/libutil.so.1 (0x00007ff7c9af4000) libz.so.1 => /lib64/libz.so.1 (0x00007ff7c98de000) libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ff7c9537000) libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ff7c91e5000) libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ff7c8e4f000) libboost_context.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_context.so.1.59.0 (0x00007ff7c8c43000) libboost_thread.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_thread.so.1.59.0 (0x00007ff7c8a21000) libboost_chrono.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_chrono.so.1.59.0 (0x00007ff7c881b000) libboost_system.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_system.so.1.59.0 (0x00007ff7c8617000) librt.so.1 => /lib64/librt.so.1 (0x00007ff7c840f000) libmpfr.so.4 => /u/eaudemard/bin/lib/libmpfr.so.4 (0x00007ff7c81b0000) libgmp.so.10 => /u/eaudemard/bin/lib/libgmp.so.10 (0x00007ff7c7f39000) libboost_thread-mt.so.5 => /usr/lib64/libboost_thread-mt.so.5 (0x00007ff7c7d24000) libboost_system-mt.so.5 => /usr/lib64/libboost_system-mt.so.5 (0x00007ff7c7b21000) /lib64/ld-linux-x86-64.so.2 (0x0000003756800000) libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ff7c69d5000)
Some libboost are linked with the good version of boost but some others are linked an oldest version (1.41). I try to fixe this with the option "--with-boost-python=" of configure but it doesn't work: ./configure --prefix=/u/eaudemard/bin/ --with-python-module-path=/u/eaudemard/bin/lib/python2.7/site-packages/ --with-boost=/soft/bioinfo/linux_RH6/boost-1.59.0/ --with-boost-libdir=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/
--with-boost-python=/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 ... checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -l/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no
You need this library installed (v 1.59.0)? Probably you it's called libboost-python, search your package repo.
checking for exit in
-lboost_python-/soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0... no checking for exit in -lboost_python... yes
ls -l /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 -rwxr-xr-x. 1 adsoft users 404020 Oct 19 13:39 /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0
After this i try apm -e of the old version and this time the configure don't find "boost_python" checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no configure: error: No usable boost::python found
Have you an idea on that point ?
Regards, Eric.
-- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. _______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
For boost, the answer was here : http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Boost was installed with another version of python, than the version used for graph-tool. It's fixed now, but the segmentation fault is still there. I will come back soon :), Eric. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi, I check and fixe all lib: ldd ~/bin/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so linux-vdso.so.1 => (0x00007ffc8f5ea000) libpython2.7.so.1.0 => /soft/bioinfo/linux_RH6/python-2.7.6/lib/libpython2.7.so.1.0 (0x00007f0ff8088000) libboost_iostreams.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_iostreams.so.1.59.0 (0x00007f0ff7e70000) libboost_python.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_python.so.1.59.0 (0x00007f0ff7c22000) libboost_regex.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_regex.so.1.59.0 (0x00007f0ff7911000) libboost_coroutine.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_coroutine.so.1.59.0 (0x00007f0ff7704000) libCGAL.so.11 => /u/eaudemard/bin/lib/libCGAL.so.11 (0x00007f0ff74db000) libexpat.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/libexpat.so.1 (0x00007f0ff72b2000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f0ff7077000) libstdc++.so.6 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libstdc++.so.6 (0x00007f0ff6d65000) libm.so.6 => /lib64/libm.so.6 (0x00007f0ff6ae1000) libc.so.6 => /lib64/libc.so.6 (0x00007f0ff674c000) libgcc_s.so.1 => /soft/bioinfo/linux_RH6/gcc-4.9.3/lib/../lib64/libgcc_s.so.1 (0x00007f0ff6536000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0ff6319000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0ff6114000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0ff5f11000) libz.so.1 => /lib64/libz.so.1 (0x00007f0ff5cfb000) librt.so.1 => /lib64/librt.so.1 (0x00007f0ff5af2000) libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007f0ff49a7000) libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007f0ff4611000) libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007f0ff42be000) libboost_context.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_context.so.1.59.0 (0x00007f0ff40b3000) libboost_thread.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_thread.so.1.59.0 (0x00007f0ff3e91000) libboost_chrono.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_chrono.so.1.59.0 (0x00007f0ff3c8a000) libboost_system.so.1.59.0 => /soft/bioinfo/linux_RH6/boost-1.59.0/lib/libboost_system.so.1.59.0 (0x00007f0ff3a87000) libmpfr.so.4 => /u/eaudemard/bin/lib/libmpfr.so.4 (0x00007f0ff3827000) libgmp.so.10 => /u/eaudemard/bin/lib/libgmp.so.10 (0x00007f0ff35b1000) And the segmentation fault is deferent (with gdb): (gdb) bt #0 0x000000339ee4406a in vfprintf () from /lib64/libc.so.6 #1 0x000000339ee69609 in vsprintf () from /lib64/libc.so.6 #2 0x000000339ee4f2b8 in sprintf () from /lib64/libc.so.6 #3 0x0000000000464451 in PyString_FromFormatV (format=0x530a57 "", vargs=0x7fffff3ff8e0) at Objects/stringobject.c:370 #4 0x000000000046491b in PyString_FromFormat (format=<value optimized out>) at Objects/stringobject.c:410 #5 0x000000000046f0ae in object_repr (self=0x6f51b10) at Objects/typeobject.c:2996 #6 0x00000000004522a5 in PyObject_Repr (v=0x6f51b10) at Objects/object.c:381 #7 0x0000000000452668 in internal_print (op=0x6f51b10, fp=0x339f18e7a0, flags=<value optimized out>, nesting=0) at Objects/object.c:305 #8 0x000000000044ccbd in dict_print (mp=0x44c993830, fp=0x339f18e7a0, flags=<value optimized out>) at Objects/dictobject.c:1063 #9 0x00000000004525a3 in internal_print (op=0x44c993830, fp=0x339f18e7a0, flags=1, nesting=0) at Objects/object.c:315 #10 0x000000000042f9d9 in file_PyObject_Print (v=<value optimized out>, f=0x7ffff7fae150, flags=1) at Objects/fileobject.c:110 #11 PyFile_WriteObject (v=<value optimized out>, f=0x7ffff7fae150, flags=1) at Objects/fileobject.c:2574 #12 0x00000000004a70d9 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:1770 #13 0x00000000004a9ab5 in fast_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4107 #14 call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4042 #15 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2666 #16 0x00000000004a9ab5 in fast_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4107 #17 call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4042 #18 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2666 The version of /lib64/libc.so come from CentOS 6: glibc-2.17-106.el7_2.1.x86_64 (compiled with gcc 4.4.7) We update your OS in 2 weeks, but do you know if this version can create an segmentation fault ? Or have you an other idea ? Regards, Eric. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 02.02.2016 19:44, Eric wrote:
We update your OS in 2 weeks, but do you know if this version can create an segmentation fault ? Or have you an other idea ?
It is impossible to say anything without the proper context. Since you haven't told us what usage pattern causes the segfault, by giving us a minimal script that reproduces it, there is nothing we can say. Note that your gdb backtrace points to functions deep inside python, that have nothing to do with graph-tool... Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi, if someone have the same error. In my case, this segmentation fault was created by a stack overflow. You can fix it temporary with : "ulimit -s unlimited", and modify your code if the segmentation fault disappear. Regards, Eric. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
participants (3)
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Eric -
Joel Moberg -
Tiago de Paula Peixoto