[cctbxbb] scitbx test crashing on mac
markus.gerstel at diamond.ac.uk
markus.gerstel at diamond.ac.uk
Sun Apr 12 23:42:42 PDT 2015
Good morning Nigel,
We throw away the base directory (and nearly everything else) each night, and then run incremental builds throughout the day. This way we can test the installer but still get build feedback in less than 10 minutes.
Cheers
Markus
From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Nigel Moriarty
Sent: 11 April 2015 00:39
To: cctbx mailing list; Paul Adams; Aaron Brewster
Subject: Re: [cctbxbb] scitbx test crashing on mac
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<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 Fri, Apr 10, 2015 at 12:46 AM, <markus.gerstel at diamond.ac.uk<mailto: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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