[cctbxbb] scitbx test crashing on mac
Nigel Moriarty
nwmoriarty at lbl.gov
Fri Apr 10 16:38:51 PDT 2015
Markus
I'm not sure what's going wrong. Our build system using building and
testing on 10.9 but my copy on 10.10 is working fine.
I have noticed a similar behaviour when the build system does not delete
both base and base_tmp directories. This rebuilds the python each time
which takes a little time but it better parallels the user experience.
I have been working on changing bootstrap.py but not sure the best way
forward.
Cheers
Nigel
---
Nigel W. Moriarty
Building 64R0246B, 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 Fri, Apr 10, 2015 at 12:46 AM, <markus.gerstel at diamond.ac.uk> wrote:
> Good morning,
>
> The test scitbx.rigid_body.proto.tst_singular has been failing
> consistently on our MacOS 10.10 system for a day now. Last known good svn
> rev. is 21989. It passes on the linux systems.
>
> Apologies if this is not the right place to report scitbx problems to.
>
> -Markus
>
>
> Stacktrace
>
> 11 Python 0x0000000100010d03 PyObject_Call + 99
>
> 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83
>
> 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81
>
> 8 libboost_python.dylib 0x0000000101a0fe5a 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 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826
>
> 6 scitbx_linalg_ext.so 0x000000010518b521 boost::python::objects::caller_py_function_impl<boost::python::detail::caller<scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<scitbx::af::shared<double>, scitbx::matrix::eigensystem::real_symmetric<double>&> > >::operator()(_object*, _object*) + 65
>
> 5 scitbx_linalg_ext.so 0x000000010518b6be _object* boost::python::detail::invoke<boost::python::to_python_value<scitbx::af::shared<double> const&>, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&> >(boost::python::detail::invoke_tag_<false, true>, boost::python::to_python_value<scitbx::af::shared<double> const&> const&, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*&)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&>&) + 46
>
> 4 ??? 0x000000010183fc20 0x0 + 4320394272
>
> 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26
>
> 2 boost_python_meta_ext.so 0x00000001005bdf80 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.
>
> Standard Error
>
> show_stack(1): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/featherstone.py(38) generalized_inverse
>
> show_stack(2): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/featherstone.py(373) FDab
>
> show_stack(3): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/test_simulation.py(28) energies_and_accelerations_update
>
> show_stack(4): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/test_simulation.py(16) __init__
>
> show_stack(5): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(72) exercise_six_dof
>
> show_stack(6): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(146) run
>
> show_stack(7): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(162) <module>
>
> libc backtrace (43 frames, most recent call last):
>
> 44 ??? 0x0000000000000003 0x0 + 3
>
> 43 Python 0x0000000100000d71 Python + 3441
>
> 42 Python 0x0000000100000e58 Python + 3672
>
> 41 Python 0x00000001000edd44 Py_Main + 3076
>
> 40 Python 0x00000001000d64a7 PyRun_SimpleFileExFlags + 711
>
> 39 Python 0x00000001000d6984 PyRun_FileExFlags + 164
>
> 38 Python 0x00000001000ad596 PyEval_EvalCode + 54
>
> 37 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 36 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111
>
> 35 Python 0x00000001000b5556 fast_function + 118
>
> 34 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 33 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111
>
> 32 Python 0x00000001000b5556 fast_function + 118
>
> 31 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 30 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651
>
> 29 Python 0x0000000100010d03 PyObject_Call + 99
>
> 28 Python 0x0000000100069e23 type_call + 339
>
> 27 Python 0x000000010006fccd slot_tp_init + 141
>
> 26 Python 0x0000000100010d03 PyObject_Call + 99
>
> 25 Python 0x000000010001e207 instancemethod_call + 247
>
> 24 Python 0x0000000100010d03 PyObject_Call + 99
>
> 23 Python 0x0000000100036a6c function_call + 364
>
> 22 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 21 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111
>
> 20 Python 0x00000001000b5556 fast_function + 118
>
> 19 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 18 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111
>
> 17 Python 0x00000001000b5556 fast_function + 118
>
> 16 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 15 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111
>
> 14 Python 0x00000001000b5556 fast_function + 118
>
> 13 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666
>
> 12 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651
>
> 11 Python 0x0000000100010d03 PyObject_Call + 99
>
> 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83
>
> 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81
>
> 8 libboost_python.dylib 0x0000000101a0fe5a 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 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826
>
> 6 scitbx_linalg_ext.so 0x000000010518b521 boost::python::objects::caller_py_function_impl<boost::python::detail::caller<scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<scitbx::af::shared<double>, scitbx::matrix::eigensystem::real_symmetric<double>&> > >::operator()(_object*, _object*) + 65
>
> 5 scitbx_linalg_ext.so 0x000000010518b6be _object* boost::python::detail::invoke<boost::python::to_python_value<scitbx::af::shared<double> const&>, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&> >(boost::python::detail::invoke_tag_<false, true>, boost::python::to_python_value<scitbx::af::shared<double> const&> const&, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*&)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&>&) + 46
>
> 4 ??? 0x000000010183fc20 0x0 + 4320394272
>
> 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26
>
> 2 boost_python_meta_ext.so 0x00000001005bdf80 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.
>
>
>
>
>
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