Am 17.02.2018 um 16:47 schrieb Alex Samuel <a...@alexsamuel.net>:
Hi there,
Sure, I'll append top of the stack. You can see our internal function
"asd::infra::util::start_of_date"; everything else is Boost, Python, or
libstdc++.
My understanding (though I haven't demonstrated this conclusively) is that, because
Python loads extension modules RTLD_GLOBAL, an extension module can pick up symbols from
another or its dependencies, even if the former "usually" satisfy relocations
from their own shared lib dependencies. So, one module linking Boost statically may
interfere with another that links it dynamically, by injecting its symbols.
If necessary I can try to put together a minimal test case, but no guarantee it
will actually trigger the bug. But it might be worth testing my theory above
first, with gdb or by some other means.
Thanks!
Alex
#0 0x00007f6ddeba4c8b in std::basic_string<char, std::char_traits<char>, std::allocator<char>
>::basic_string(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/numexpr/../../../libstdc++.so.6
#1 0x00007f6dd4f978d6 in
boost::re_detail::cpp_regex_traits_char_layer<char>::init() ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../.././libboost_regex.so.1.55.0
#2 0x00007f6dd4fdbd88 in boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>,
boost::re_detail::cpp_regex_traits_implementation<char>
>::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../.././libboost_regex.so.1.55.0
#3 0x00007f6dd4fe5bb5 in boost::basic_regex<char, boost::regex_traits<char,
boost::cpp_regex_traits<char> > >::do_assign(char const*, char const*, unsigned int)
()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../.././libboost_regex.so.1.55.0
#4 0x00007f6dd575a90e in asd::infra::util::start_of_date(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, char const*) ()
at
/prod/sys/sysasd/opt/tudor-devtools/v1.3/Linux.el6.x86_64-corei7-avx-gcc4.83-anaconda2.0.1/include/boost/regex/v4/basic_regex.hpp:382
#5 0x00007f6dd2c36734 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned long
(*)(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*),
boost::python::default_call_policies, boost::mpl::vector3<unsigned long, std::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, char const*> > >::operator()(_object*, _object*) ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/util.so
#6 0x00007f6dd52ac71a in boost::python::objects::function::call(_object*,
_object*) const ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../../libboost_python.so.1.55.0
#7 0x00007f6dd52aca68 in
boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous
namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&)
()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../../libboost_python.so.1.55.0
#8 0x00007f6dd52b4cd3 in
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../../libboost_python.so.1.55.0
#9 0x00007f6dd2c32c03 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<asd::infra::Exception, void (*)(asd::infra::Exception const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(asd::infra::Exception 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
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/util.so
#10 0x00007f6dd52b4a9d in
boost::python::handle_exception_impl(boost::function0<void>) ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../../libboost_python.so.1.55.0
#11 0x00007f6dd52ab2b3 in function_call ()
from
/space/asd/conda/envs/rd-20180212-0/lib/python2.7/site-packages/asd/infra/../../../../libboost_python.so.1.55.0
#12 0x00007f6df2bc8e93 in PyObject_Call (func=0x2799850, arg=<value optimized
out>,
kw=<value optimized out>) at Objects/abstract.c:2547
#13 0x00007f6df2c7b80d in do_call (f=<value optimized out>, throwflag=<value
optimized out>)
at Python/ceval.c:4569
#14 call_function (f=<value optimized out>, throwflag=<value optimized out>) at
Python/ceval.c:4374
#15 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized
out>) at Python/ceval.c:2989
On 02/17/2018 10:31 AM, Uwe L. Korn wrote:
Hello,
I am not sure why we are linking statically in the conda-forge packages, as a
gut feeling we should link dynamically there. Wes, can you remember why?
Alex, would it be possible for you to send us the part of the segmentation
fault that is not private to your modules. That would be a good indicator for
us what is going wrong.
Typically it is best when you enable coredumps with `ulimit -c unlimited` and
then run your program as usual. There should be no performance penalty. When
ist segfaults, run `gdb python core` (note that the core file might also be
postfixed with the PID but that depends on your system). In gdb type 'thread
apply all bt full'. Post thd output pf that command and strip away the parts we
should not see. Most relevant will be the stacktrace of the thread that
segfaulted.
Uwe
Am 16.02.2018 um 23:17 schrieb Alex Samuel <a...@alexsamuel.net>:
Hello,
I am having some troubles using the Continuum PyArrow conda package
dependencies in conjunction with internal C++ extension modules.
Apparently, Arrow and Parquet link Boost statically. We have some internal
packages containing C++ code that linking Boost libs dynamicaly. If we import
Feather as well as our own extension modules into the same Python process, we
get random segfaults in Boost. I think what's happening is that our extension
modules are picking up Boost's symbols from Arrow and Parquet already loaded
into the process, rather than from our own Boost shared libs.
Could anyone explain the policy for linking Boost in binary distributions,
particularly conda packages? What is your expectation for how other C++
extension modules should be built?
Thanks in advance,
Alex
