[cctbxbb] Boost Python 1.56

Marcin Wojdyr wojdyr at gmail.com
Mon Feb 15 10:56:14 PST 2016


To summarize:
I did this exercise on Ubuntu 14.04 with python from Anaconda. Using
Boost from boost.gz from LBL I get 3 errors when running
cctbx_regression.test_nightly (copied below - I don't know what's the
reason).
Boost 1.60 has a regression seemingly caused by changes in
boost.traits. It may be trivial to fix for someone familiar with
boost.python internals, but I'm not such person and boost.python is
not actively maintained nowadays, so I gave up.
Boost 1.59 also has one regression in boost python, but it's already fixed:
https://github.com/boostorg/python/issues/39

With this version (1.59 + patch from #39) I get additional two test
failures caused by changed (improved)
boost/random/normal_distribution.hpp:
https://github.com/boostorg/random/commit/f0ec97ba36c05ef00f2d29dcf66094e3f4abdcde
The failing tests just expect different pseudo-random values, so it
shouldn't matter.
You may consider using this version.
Now I'm updating CCP4 development builds to this and we'll see if we
see other problems.

Marcin



libtbx.python "/home/marcin/dials/modules/cctbx_project/cctbx/translation_search/boost_python/tst_translation_search.py"
[FAIL]
  Time:  0.38
  Return code: 1
  OKs: 0
  Standard error:
    show_stack(1):
/home/marcin/dials/modules/cctbx_project/cctbx/translation_search/boost_python/tst_translation_search.py(31)
exercise_fast_nv1995
    show_stack(2):
/home/marcin/dials/modules/cctbx_project/cctbx/translation_search/boost_python/tst_translation_search.py(51)
run
    show_stack(3):
/home/marcin/dials/modules/cctbx_project/cctbx/translation_search/boost_python/tst_translation_search.py(56)
<module>
    libc backtrace (28 frames, most recent call last):
      /home/marcin/dials/build/../../miniconda2/bin/python2.7() [0x400649]
      /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fbafe28fec5]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(Py_Main+0xca4)
[0x7fbaff091b74]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xef)
[0x7fbaff07c22f]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xb0)
[0x7fbaff07c050]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)
[0x7fbaff05bb42]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)
[0x7fbaff05ba2e]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8525)
[0x7fbaff05aa55]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)
[0x7fbaff05ba2e]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8525)
[0x7fbaff05aa55]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)
[0x7fbaff05ba2e]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a24)
[0x7fbaff058f54]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53)
[0x7fbafefa7d23]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(+0xacdd8)
[0x7fbaff00add8]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(+0xb6320)
[0x7fbaff014320]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53)
[0x7fbafefa7d23]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(+0x5c4bf)
[0x7fbafefba4bf]
      /home/marcin/miniconda2/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53)
[0x7fbafefa7d23]
      /home/marcin/dials/build/lib/libboost_python.so(+0x280d3) [0x7fbafcd9e0d3]
      /home/marcin/dials/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x53)
[0x7fbafcda96d3]
      /home/marcin/dials/build/lib/libboost_python.so(+0x29918) [0x7fbafcd9f918]
      /home/marcin/dials/build/lib/libboost_python.so(boost::python::objects::function::call(_object*,
_object*) const+0xca) [0x7fbafcd9f5aa]
      /home/marcin/dials/build/lib/cctbx_translation_search_ext.so(boost::python::detail::caller_arity<9u>::impl<void
(*)(_object*, scitbx::af::tiny<int, 3ul> const&,
cctbx::sgtbx::space_group const&, bool,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor>), boost::python::default_call_policies,
boost::mpl::vector10<void, _object*, scitbx::af::tiny<int, 3ul>
const&, cctbx::sgtbx::space_group const&, bool,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> > >::operator()(_object*,
_object*)+0x3d8) [0x7fbae12f8628]
      /home/marcin/dials/build/lib/cctbx_translation_search_ext.so(boost::python::objects::make_holder<8>::apply<boost::python::objects::value_holder<cctbx::translation_search::fast_nv1995<double>
>, boost::mpl::vector8<scitbx::af::tiny<int, 3ul> const&,
cctbx::sgtbx::space_group const&, bool,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> > >::execute(_object*,
scitbx::af::tiny<int, 3ul> const&, cctbx::sgtbx::space_group const&,
bool, scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor>)+0x91) [0x7fbae12f81f1]
      /home/marcin/dials/build/lib/cctbx_translation_search_ext.so(cctbx::translation_search::fast_nv1995<double>::fast_nv1995(scitbx::af::tiny<int,
3ul> const&, cctbx::sgtbx::space_group const&, bool,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<cctbx::miller::index<int>,
scitbx::af::trivial_accessor> const&,
scitbx::af::const_ref<std::complex<double>,
scitbx::af::trivial_accessor> const&)+0xa37) [0x7fbae12f7d57]
      /home/marcin/dials/build/lib/cctbx_translation_search_ext.so(void
cctbx::translation_search::fast_nv1995_detail::combination_eq12<double>(scitbx::af::const_ref<double,
scitbx::af::c_grid_padded<3ul, unsigned long> > const&,
scitbx::af::ref<double, scitbx::af::c_grid<3ul, unsigned long> >
const&, double const&)+0x169) [0x7fbae12eece9]
      /lib/x86_64-linux-gnu/libc.so.6(+0x36d40) [0x7fbafe2a4d40]
      /home/marcin/dials/build/lib/boost_python_meta_ext.so(+0x18140)
[0x7fbafcfdc140]
    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 "/home/marcin/dials/modules/cctbx_project/cctbx/regression/tst_miller_merge_equivalents.py"
P31 [FAIL]
  Time:  0.35
  Return code: 1
  OKs: 0
  Standard error:
    Traceback (most recent call last):
      File "/home/marcin/dials/modules/cctbx_project/cctbx/regression/tst_miller_merge_equivalents.py",
line 157, in <module>
        run()
      File "/home/marcin/dials/modules/cctbx_project/cctbx/regression/tst_miller_merge_equivalents.py",
line 152, in run
        exercise_split_unmerged()
      File "/home/marcin/dials/modules/cctbx_project/cctbx/regression/tst_miller_merge_equivalents.py",
line 144, in exercise_split_unmerged
        eps=0.05)
    AssertionError
libtbx.python "/home/marcin/dials/modules/cctbx_project/iotbx/mtz/tst_ext.py"
[FAIL]
  Time:  0.54
  Return code: 1
  OKs: 0
  Standard error:
    Traceback (most recent call last):
      File "/home/marcin/dials/modules/cctbx_project/iotbx/mtz/tst_ext.py",
line 1383, in <module>
        run()
      File "/home/marcin/dials/modules/cctbx_project/iotbx/mtz/tst_ext.py",
line 1379, in run
        exercise()
      File "/home/marcin/dials/modules/cctbx_project/iotbx/mtz/tst_ext.py",
line 1366, in exercise
        exercise_modifiers(verbose=command_line.options.verbose)
      File "/home/marcin/dials/modules/cctbx_project/iotbx/mtz/tst_ext.py",
line 1093, in exercise_modifiers
        assert approx_equal(v, [-1]*4)
    AssertionError


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