[cctbxbb] Boost broken on mac?
Nigel Moriarty
nwmoriarty at lbl.gov
Thu Mar 24 08:28:09 PDT 2016
Markus
It seems a little odd that Boost is the problem because it has not changed
for a very long time. In my experience, this usually means that the code
using Boost has a memory leak.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Mar 24, 2016 at 8:05 AM, <markus.gerstel at diamond.ac.uk> wrote:
> Dials west is currently observing test failures on Mac related to Boost.
>
> To exclude any errors on our side I have run things twice clean from
> bootstrap:
>
> One of a number of affected tests:
>
>
>
> libtbx.python cctbx/xray/boost_python/tst_xray.py
>
>
>
> show_stack(1):
> /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(381)
> exercise_conversions
>
> show_stack(2):
> /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(1993)
> run
>
> show_stack(3):
> /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(2009)
> <module>
>
> libc backtrace (29 frames, most recent call last):
>
> 30 Python 0x0000000100000d71 Python + 3441
>
> 29 Python 0x0000000100000e58 Python + 3672
>
> 28 Python 0x00000001000ef06f Py_Main +
> 3135
>
> 27 Python 0x00000001000d78be
> PyRun_SimpleFileExFlags + 702
>
> 26 Python 0x00000001000d7d84
> PyRun_FileExFlags + 164
>
> 25 Python 0x00000001000aea06
> PyEval_EvalCode + 54
>
> 24 Python 0x00000001000af244
> PyEval_EvalCodeEx + 2100
>
> 23 Python 0x00000001000b25c8
> PyEval_EvalFrameEx + 12280
>
> 22 Python 0x00000001000b6ab6 fast_function
> + 118
>
> 21 Python 0x00000001000af244
> PyEval_EvalCodeEx + 2100
>
> 20 Python 0x00000001000b25c8
> PyEval_EvalFrameEx + 12280
>
> 19 Python 0x00000001000b6ab6 fast_function
> + 118
>
> 18 Python 0x00000001000af244
> PyEval_EvalCodeEx + 2100
>
> 17 Python 0x00000001000b4198
> PyEval_EvalFrameEx + 19400
>
> 16 Python 0x0000000100011023 PyObject_Call
> + 99
>
> 15 Python 0x000000010006ad8b type_call + 347
>
> 14 Python 0x00000001000708af slot_tp_init
> + 175
>
> 13 Python 0x0000000100011023 PyObject_Call
> + 99
>
> 12 Python 0x000000010001f0d8
> instancemethod_call + 232
>
> 11 Python 0x0000000100011023 PyObject_Call
> + 99
>
> 10 libboost_python.dylib 0x0000000101888663
> boost::python::objects::function_call(_object*, _object*, _object*) + 83
>
> 9 libboost_python.dylib 0x000000010188ce71
> boost::python::handle_exception_impl(boost::function0<void>) + 81
>
> 8 libboost_python.dylib 0x00000001018889ca
> boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous
> namespace)::bind_return,
> void>::invoke(boost::detail::function::function_buffer&) + 26
>
> 7 libboost_python.dylib 0x000000010188693a
> boost::python::objects::function::call(_object*, _object*) const + 874
>
> 6 cctbx_xray_ext.so 0x0000000107c8e1c5
> boost::python::detail::caller_arity<3u>::impl<void (*)(_object*,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&),
> boost::python::default_call_policies, boost::mpl::vector4<void, _object*,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&>
> >::operator()(_object*, _object*) + 229
>
> 5 cctbx_xray_ext.so 0x0000000107c91f44
> boost::python::objects::make_holder<2>::apply<boost::python::objects::value_holder<cctbx::xray::array_f_sq_as_f<cctbx::xray::f_sq_as_f_xtal_3_7,
> double> >,
> boost::mpl::joint_view<boost::python::detail::drop1<boost::python::detail::type_list<scitbx::af::const_ref<double,
> scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
> scitbx::af::trivial_accessor> const&, boost::python::optional<double
> const&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_> >, boost::python::optional<double
> const&, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_,
> mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_> > >::execute(_object*,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&,
> scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&) + 100
>
> 4 ??? 0x0000000000000002 0x0 + 2
>
> 3 libsystem_platform.dylib 0x00007fff8caabeaa _sigtramp + 26
>
> 2 boost_python_meta_ext.so 0x0000000101841370
> initboost_python_meta_ext + 0
>
> Floating-point error (Python and libc call stacks above)
>
> This crash may be due to a problem in any imported
>
> Python module, including modules which are not part
>
> of the cctbx project. To disable the traps leading
>
> to this message, define these environment variables
>
> (e.g. assign the value 1):
>
> BOOST_ADAPTBX_FPE_DEFAULT
>
> BOOST_ADAPTBX_SIGNALS_DEFAULT
>
> This will NOT solve the problem, just mask it, but
>
> may allow you to proceed in case it is not critical.
>
>
>
>
>
> Any ideas?
>
>
>
> Best wishes,
>
> -Markus
>
>
>
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