[cctbxbb] Boost broken on mac?
Hattne, Johan
hattnej at janelia.hhmi.org
Wed Apr 6 08:33:07 PDT 2016
Does the problem go away with less aggressive optimization? If I recall correctly this is built with -O3 by default, which I don’t think is actually guaranteed not to break your code.
// Johan
> On Apr 6, 2016, at 11:20, richard.gildea at diamond.ac.uk wrote:
>
> I think this is a problem caused by the latest Xcode 7.3 update, released 2016-03-21 (the date the update was applied according to the App Store update history coincides with the time our mac builds became broken):
>
> https://developer.apple.com/library/ios/releasenotes/DeveloperTools/RN-Xcode/RevisionHistory.html#//apple_ref/doc/uid/TP40001051-CH99-SW1
>
> I have reproduced the issue with the standard cctbx build using the bootstrap script as follows:
>
> $ svn export svn://svn.code.sf.net/p/cctbx/code/trunk/libtbx/auto_build/bootstrap.py
> $ python bootstrap.py --builder=cctbx --nproc=8
> $ source build/setpaths.sh
> $ libtbx.python ../modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py
> show_stack(1): ../modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(381) exercise_conversions
> show_stack(2): ../modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(1993) run
> show_stack(3): ../modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(2009) <module>
> libc backtrace (30 frames, most recent call last):
> 31 ??? 0x0000000000000003 0x0 + 3
> 30 Python 0x0000000100000d71 Python + 3441
> 29 Python 0x0000000100000e58 Python + 3672
> 28 Python 0x00000001000ef08f Py_Main + 3135
> 27 Python 0x00000001000d78de PyRun_SimpleFileExFlags + 702
> 26 Python 0x00000001000d7da4 PyRun_FileExFlags + 164
> 25 Python 0x00000001000aea26 PyEval_EvalCode + 54
> 24 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 23 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 22 Python 0x00000001000b6ad6 fast_function + 118
> 21 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 20 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 19 Python 0x00000001000b6ad6 fast_function + 118
> 18 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 17 Python 0x00000001000b41b8 PyEval_EvalFrameEx + 19400
> 16 Python 0x0000000100011043 PyObject_Call + 99
> 15 Python 0x000000010006adab type_call + 347
> 14 Python 0x00000001000708cf slot_tp_init + 175
> 13 Python 0x0000000100011043 PyObject_Call + 99
> 12 Python 0x000000010001f0f8 instancemethod_call + 232
> 11 Python 0x0000000100011043 PyObject_Call + 99
> 10 libboost_python.dylib 0x0000000101a88663 boost::python::objects::function_call(_object*, _object*, _object*) + 83
> 9 libboost_python.dylib 0x0000000101a8ce71 boost::python::handle_exception_impl(boost::function0<void>) + 81
> 8 libboost_python.dylib 0x0000000101a889ca 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 0x0000000101a8693a boost::python::objects::function::call(_object*, _object*) const + 874
> 6 cctbx_xray_ext.so 0x000000010748ba55 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 0x000000010748f7d4 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 libunwind.dylib 0x00007fff86be8404 _Unwind_GetRegionStart + 17
> 3 libsystem_platform.dylib 0x00007fff89b59eaa _sigtramp + 26
> 2 boost_python_meta_ext.so 0x0000000101a413d0 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.
>
> I have narrowed this down to what looks like a case of compiler over-optimisation at line 41 of cctbx/xray/conversions.h. Replacing:
>
> if (f_sq > 0) f = std::sqrt(f_sq);
> else f = 0;
>
> with:
>
> if (f_sq <= 0) {
> f = 0;
> }
> else {
> CCTBX_ASSERT(f_sq > 0);
> f = std::sqrt(f_sq);
> }
>
> Causes the error to disappear.
>
> However there are a number of other errors that are potentially more concerning, including some that result in different output rather than a floating point exception, which will likely be harder to debug:
>
> $ libtbx.run_tests_parallel module=scitbx module=cctbx module=iotbx nproc=8 run_in_tmp_dir=True
> Error: the following jobs returned non-zero exit codes or suspicious stderr output:
>
> libtbx.python "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py" [FAIL]
> Time: 14.01
> Return code: 1
> OKs: 0
> Standard error:
> Traceback (most recent call last):
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py", line 159, in <module>
> run(sys.argv[1:])
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py", line 154, in run
> compare_implementations()
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py", line 130, in compare_implementations
> this_script=this_script, n=n, m=m, iprint=[iprint1, iprint2])
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py", line 117, in run_and_compare_implementations
> assert not show_diff(a, b)
> AssertionError
> libtbx.python "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py" [FAIL]
> Time: 1.04
> Return code: 1
> OKs: 0
> Standard error:
> show_stack(1): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(381) exercise_conversions
> show_stack(2): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(1993) run
> show_stack(3): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/xray/boost_python/tst_xray.py(2009) <module>
> libc backtrace (30 frames, most recent call last):
> 31 ??? 0x0000000000000003 0x0 + 3
> 30 Python 0x0000000100000d71 Python + 3441
> 29 Python 0x0000000100000e58 Python + 3672
> 28 Python 0x00000001000ef08f Py_Main + 3135
> 27 Python 0x00000001000d78de PyRun_SimpleFileExFlags + 702
> 26 Python 0x00000001000d7da4 PyRun_FileExFlags + 164
> 25 Python 0x00000001000aea26 PyEval_EvalCode + 54
> 24 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 23 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 22 Python 0x00000001000b6ad6 fast_function + 118
> 21 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 20 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 19 Python 0x00000001000b6ad6 fast_function + 118
> 18 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 17 Python 0x00000001000b41b8 PyEval_EvalFrameEx + 19400
> 16 Python 0x0000000100011043 PyObject_Call + 99
> 15 Python 0x000000010006adab type_call + 347
> 14 Python 0x00000001000708cf slot_tp_init + 175
> 13 Python 0x0000000100011043 PyObject_Call + 99
> 12 Python 0x000000010001f0f8 instancemethod_call + 232
> 11 Python 0x0000000100011043 PyObject_Call + 99
> 10 libboost_python.dylib 0x0000000101e85663 boost::python::objects::function_call(_object*, _object*, _object*) + 83
> 9 libboost_python.dylib 0x0000000101e89e71 boost::python::handle_exception_impl(boost::function0<void>) + 81
> 8 libboost_python.dylib 0x0000000101e859ca 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 0x0000000101e8393a boost::python::objects::function::call(_object*, _object*) const + 874
> 6 cctbx_xray_ext.so 0x0000000107c4da55 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 0x0000000107c517d4 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 ??? 0x0000000000000005 0x0 + 5
> 3 libsystem_platform.dylib 0x00007fff89b59eaa _sigtramp + 26
> 2 boost_python_meta_ext.so 0x0000000101e3e3d0 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.
> libtbx.python "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/maptbx/boost_python/tst_maptbx.py" [FAIL]
> Time: 4.96
> Return code: 1
> OKs: 0
> Standard error:
> Traceback (most recent call last):
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/maptbx/boost_python/tst_maptbx.py", line 1395, in <module>
> run(args=sys.argv[1:])
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/maptbx/boost_python/tst_maptbx.py", line 1373, in run
> exercise_misc()
> File "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/maptbx/boost_python/tst_maptbx.py", line 365, in exercise_misc
> assert (approx_equal(stats.min, 8.3, eps=0.1))
> AssertionError
> libtbx.python "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/regression/tst_miller.py" P31 [FAIL]
> Time: 12.97
> Return code: 1
> OKs: 0
> Standard error:
> show_stack(1): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/miller/__init__.py(2300) f_sq_as_f
> show_stack(2): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/miller/__init__.py(2343) as_amplitude_array
> show_stack(3): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/miller/__init__.py(2276) enforce_positive_amplitudes
> show_stack(4): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/regression/tst_miller.py(197) exercise_enforce_positive_amplitudes
> show_stack(5): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/regression/tst_miller.py(2398) run
> show_stack(6): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/regression/tst_miller.py(2415) <module>
> libc backtrace (38 frames, most recent call last):
> 39 Python 0x0000000100000d71 Python + 3441
> 38 Python 0x0000000100000e58 Python + 3672
> 37 Python 0x00000001000ef08f Py_Main + 3135
> 36 Python 0x00000001000d78de PyRun_SimpleFileExFlags + 702
> 35 Python 0x00000001000d7da4 PyRun_FileExFlags + 164
> 34 Python 0x00000001000aea26 PyEval_EvalCode + 54
> 33 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 32 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 31 Python 0x00000001000b6ad6 fast_function + 118
> 30 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 29 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 28 Python 0x00000001000b6ad6 fast_function + 118
> 27 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 26 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 25 Python 0x00000001000b6ad6 fast_function + 118
> 24 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 23 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 22 Python 0x00000001000b6ad6 fast_function + 118
> 21 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 20 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 19 Python 0x00000001000b6ad6 fast_function + 118
> 18 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 17 Python 0x00000001000b41b8 PyEval_EvalFrameEx + 19400
> 16 Python 0x0000000100011043 PyObject_Call + 99
> 15 Python 0x000000010006adab type_call + 347
> 14 Python 0x00000001000708cf slot_tp_init + 175
> 13 Python 0x0000000100011043 PyObject_Call + 99
> 12 Python 0x000000010001f0f8 instancemethod_call + 232
> 11 Python 0x0000000100011043 PyObject_Call + 99
> 10 libboost_python.dylib 0x000000010270f663 boost::python::objects::function_call(_object*, _object*, _object*) + 83
> 9 libboost_python.dylib 0x0000000102713e71 boost::python::handle_exception_impl(boost::function0<void>) + 81
> 8 libboost_python.dylib 0x000000010270f9ca 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 0x000000010270d93a boost::python::objects::function::call(_object*, _object*) const + 874
> 6 cctbx_xray_ext.so 0x00000001083e7f7b boost::python::detail::caller_arity<4u>::impl<void (*)(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, double const&), boost::python::default_call_policies, boost::mpl::vector5<void, _object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, double const&> >::operator()(_object*, _object*) + 347
> 5 cctbx_xray_ext.so 0x00000001083e7d47 boost::python::objects::make_holder<3>::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&, double const&) + 87
> 4 ??? 0x0000000000000000 0x0 + 0
> 3 libsystem_platform.dylib 0x00007fff89b59eaa _sigtramp + 26
> 2 boost_python_meta_ext.so 0x00000001025813d0 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.
> libtbx.python "/Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/regression/tst_reflection_file_editor.py" [FAIL]
> Time: 1.64
> Return code: 1
> OKs: 0
> Standard error:
> show_stack(1): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/cctbx/miller/__init__.py(2300) f_sq_as_f
> show_stack(2): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/reflection_file_editor.py(1167) modify_experimental_data_array
> show_stack(3): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/reflection_file_editor.py(1034) modify_array
> show_stack(4): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/reflection_file_editor.py(525) __init__
> show_stack(5): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/regression/tst_reflection_file_editor.py(60) run_and_reload
> show_stack(6): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/regression/tst_reflection_file_editor.py(67) exercise_basic
> show_stack(7): /Users/rjgildea/tmp/tst_bootstrap/tmp/modules/cctbx_project/iotbx/regression/tst_reflection_file_editor.py(901) <module>
> libc backtrace (48 frames, most recent call last):
> 49 ??? 0x0000000000000003 0x0 + 3
> 48 Python 0x0000000100000d71 Python + 3441
> 47 Python 0x0000000100000e58 Python + 3672
> 46 Python 0x00000001000ef08f Py_Main + 3135
> 45 Python 0x00000001000d78de PyRun_SimpleFileExFlags + 702
> 44 Python 0x00000001000d7da4 PyRun_FileExFlags + 164
> 43 Python 0x00000001000aea26 PyEval_EvalCode + 54
> 42 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 41 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 40 Python 0x00000001000b6ad6 fast_function + 118
> 39 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 38 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 37 Python 0x00000001000b6ad6 fast_function + 118
> 36 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 35 Python 0x00000001000b41b8 PyEval_EvalFrameEx + 19400
> 34 Python 0x0000000100011043 PyObject_Call + 99
> 33 Python 0x000000010006adab type_call + 347
> 32 Python 0x00000001000708cf slot_tp_init + 175
> 31 Python 0x0000000100011043 PyObject_Call + 99
> 30 Python 0x000000010001f0f8 instancemethod_call + 232
> 29 Python 0x0000000100011043 PyObject_Call + 99
> 28 Python 0x0000000100037b7b function_call + 363
> 27 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 26 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 25 Python 0x00000001000b6ad6 fast_function + 118
> 24 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 23 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 22 Python 0x00000001000b6ad6 fast_function + 118
> 21 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 20 Python 0x00000001000b25e8 PyEval_EvalFrameEx + 12280
> 19 Python 0x00000001000b6ad6 fast_function + 118
> 18 Python 0x00000001000af264 PyEval_EvalCodeEx + 2100
> 17 Python 0x00000001000b41b8 PyEval_EvalFrameEx + 19400
> 16 Python 0x0000000100011043 PyObject_Call + 99
> 15 Python 0x000000010006adab type_call + 347
> 14 Python 0x00000001000708cf slot_tp_init + 175
> 13 Python 0x0000000100011043 PyObject_Call + 99
> 12 Python 0x000000010001f0f8 instancemethod_call + 232
> 11 Python 0x0000000100011043 PyObject_Call + 99
> 10 libboost_python.dylib 0x0000000101b0f663 boost::python::objects::function_call(_object*, _object*, _object*) + 83
> 9 libboost_python.dylib 0x0000000101b13e71 boost::python::handle_exception_impl(boost::function0<void>) + 81
> 8 libboost_python.dylib 0x0000000101b0f9ca 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 0x0000000101b0d93a boost::python::objects::function::call(_object*, _object*) const + 874
> 6 cctbx_xray_ext.so 0x00000001084eef7b boost::python::detail::caller_arity<4u>::impl<void (*)(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, double const&), boost::python::default_call_policies, boost::mpl::vector5<void, _object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> const&, double const&> >::operator()(_object*, _object*) + 347
> 5 cctbx_xray_ext.so 0x00000001084eed47 boost::python::objects::make_holder<3>::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&, double const&) + 87
> 4 ??? 0x000000010a526948 0x0 + 4468140360
> 3 libsystem_platform.dylib 0x00007fff89b59eaa _sigtramp + 26
> 2 boost_python_meta_ext.so 0x00000001019413d0 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.
>
> Please verify these tests manually.
>
> Summary:
> Tests run : 336
> Failures : 5
> Warnings (possible failures) : 0
> Stderr output (discouraged) : 5
>
> See run_tests_parallel_zlog for full output.
>
> In particular, there is different output for the lbfgs comparisons to the fortran implementation (fortran output remains same, both raw and raw_reference cpp outputs differ from fortran):
>
> $ scitbx.python "/Users/rjgildea/tmp/tst_bootstrap/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py" fortran 14 2 2 0
> *************************************************
> N= 14 NUMBER OF CORRECTIONS= 2
> INITIAL VALUES
> F= 1.694D+02 GNORM= 6.161D+02
> *************************************************
>
> I NFN FUNC GNORM STEPLENGTH
>
> 1 2 1.476D+02 4.302D+02 1.623D-03
> 3 4 2.908D+01 2.874D+01 1.000D+00
> 5 8 2.826D+01 9.851D+00 2.100D+01
> 7 10 2.494D+01 4.485D+01 1.000D+00
> 9 17 5.456D+00 6.382D+00 1.406D+00
> 11 20 4.682D+00 4.658D+00 1.000D+00
> 13 23 3.360D+00 2.641D+01 1.000D+00
> 15 25 1.727D+00 2.826D+00 1.000D+00
> 17 28 1.291D+00 1.311D+01 1.000D+00
> 19 31 5.774D-01 7.928D+00 4.048D-01
> 21 33 3.185D-01 1.783D+01 1.000D+00
> 23 35 6.065D-02 3.459D+00 1.000D+00
> 25 37 2.849D-02 3.223D+00 1.000D+00
> 27 40 1.306D-02 1.305D-01 6.670D-02
> 29 42 2.974D-04 6.588D-01 1.000D+00
> 31 45 1.823D-06 1.125D-02 1.000D+00
> 33 48 5.604D-10 1.497D-04 2.447D-02
> 34 49 5.059D-15 4.741D-07 1.000D+00
>
> THE MINIMIZATION TERMINATED WITHOUT DETECTING ERRORS.
> IFLAG = 0
>
> $ scitbx.python "/Users/rjgildea/tmp/tst_bootstrap/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py" raw 14 2 2 0
> *************************************************
> N= 14 NUMBER OF CORRECTIONS= 2
> INITIAL VALUES
> F= 1.694E+02 GNORM= 6.161E+02
> *************************************************
>
> I NFN FUNC GNORM STEPLENGTH
>
> 1 2 1.476E+02 4.302E+02 1.623E-03
> 3 4 2.908E+01 2.874E+01 1.000E+00
> 5 8 2.826E+01 9.851E+00 2.100E+01
> 7 10 2.494E+01 4.485E+01 1.000E+00
> 9 17 5.456E+00 6.382E+00 1.406E+00
> 11 20 4.682E+00 4.658E+00 1.000E+00
> 13 23 3.360E+00 2.641E+01 1.000E+00
> 15 25 1.727E+00 2.826E+00 1.000E+00
> 17 28 1.291E+00 1.311E+01 1.000E+00
> 19 31 5.774E-01 7.928E+00 4.048E-01
> 21 33 3.185E-01 1.783E+01 1.000E+00
> 23 35 6.065E-02 3.459E+00 1.000E+00
> 25 37 2.849E-02 3.223E+00 1.000E+00
> 27 40 1.306E-02 1.305E-01 6.670E-02
> 29 42 2.974E-04 6.588E-01 1.000E+00
> 31 45 1.823E-06 1.125E-02 1.000E+00
> 33 48 5.603E-10 1.498E-04 2.447E-02
> 34 49 5.060E-15 4.757E-07 1.000E+00
>
> THE MINIMIZATION TERMINATED WITHOUT DETECTING ERRORS.
> IFLAG = 0
>
> $ scitbx.python "/Users/rjgildea/tmp/tst_bootstrap/modules/cctbx_project/scitbx/lbfgs/tst_lbfgs_fem.py" raw_reference 14 2 2 0
> *************************************************
> N= 14 NUMBER OF CORRECTIONS= 2
> INITIAL VALUES
> F= 1.694E+02 GNORM= 6.161E+02
> *************************************************
>
> I NFN FUNC GNORM STEPLENGTH
>
> 1 2 1.476E+02 4.302E+02 1.623E-03
> 3 4 2.908E+01 2.874E+01 1.000E+00
> 5 8 2.826E+01 9.851E+00 2.100E+01
> 7 10 2.494E+01 4.485E+01 1.000E+00
> 9 17 5.456E+00 6.382E+00 1.406E+00
> 11 20 4.682E+00 4.658E+00 1.000E+00
> 13 23 3.360E+00 2.641E+01 1.000E+00
> 15 25 1.727E+00 2.826E+00 1.000E+00
> 17 28 1.291E+00 1.311E+01 1.000E+00
> 19 31 5.774E-01 7.928E+00 4.048E-01
> 21 33 3.185E-01 1.783E+01 1.000E+00
> 23 35 6.065E-02 3.459E+00 1.000E+00
> 25 37 2.849E-02 3.223E+00 1.000E+00
> 27 40 1.306E-02 1.305E-01 6.670E-02
> 29 42 2.974E-04 6.588E-01 1.000E+00
> 31 45 1.823E-06 1.125E-02 1.000E+00
> 33 48 5.603E-10 1.498E-04 2.447E-02
> 34 49 5.060E-15 4.757E-07 1.000E+00
>
> THE MINIMIZATION TERMINATED WITHOUT DETECTING ERRORS.
> IFLAG = 0
>
> Testing on Linux, the raw and raw_reference give identical output to the fortran output above. Does anyone have any ideas how best to resolve these issues?
>
> Cheers,
>
> Richard
>
>
> On 24 Mar 2016, at 15:28, Nigel Moriarty <nwmoriarty at lbl.gov<mailto:nwmoriarty at lbl.gov>> wrote:
>
> 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<tel:510-486-5709> Email : NWMoriarty at LBL.gov<mailto:NWMoriarty at lbl.gov>
> Fax : 510-486-5909<tel:510-486-5909> Web : CCI.LBL.gov<http://cci.lbl.gov/>
>
> On Thu, Mar 24, 2016 at 8:05 AM, <markus.gerstel at diamond.ac.uk<mailto: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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