[cctbxbb] Boost broken on mac?
richard.gildea at diamond.ac.uk
richard.gildea at diamond.ac.uk
Wed Apr 6 08:20:41 PDT 2016
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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