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@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Fri, Apr 10, 2015 at 12:46 AM, <markus.gerstel@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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