[cctbxbb] Failing tests on python3 builds

richard.gildea at diamond.ac.uk richard.gildea at diamond.ac.uk
Mon Jul 29 07:48:49 PDT 2019

This also fails for me on my local (python 2.7) mac build. I have taken the liberty of creating a github ticket for this test failure:


Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
OX11 0DE
From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org> on behalf of Graeme.Winter at Diamond.ac.uk <Graeme.Winter at diamond.ac.uk>
Sent: 29 July 2019 15:39:54
To: cctbx mailing list
Subject: Re: [cctbxbb] Failing tests on python3 builds

Well raised

I thought something was very wrong as the 2.7 build failed on OS X but then looking the error was:

Error: the following jobs returned non-zero exit codes or suspicious stderr output:

libtbx.python "/Users/vsts/agent/2.154.3/work/1/modules/cctbx_project/scitbx/math/tests/tst_math.py" [FAIL] 1.2s
  Time:  1.24
  Return code: 1
  OKs: 0
  Standard error:
    show_stack(1): /Users/vsts/agent/2.154.3/work/1/modules/cctbx_project/scitbx/math/tests/tst_math.py(495) check_lambertw
    show_stack(2): /Users/vsts/agent/2.154.3/work/1/modules/cctbx_project/scitbx/math/tests/tst_math.py(510) exercise_lambertw
    show_stack(3): /Users/vsts/agent/2.154.3/work/1/modules/cctbx_project/scitbx/math/tests/tst_math.py(2041) run
    show_stack(4): /Users/vsts/agent/2.154.3/work/1/modules/cctbx_project/scitbx/math/tests/tst_math.py(2066) <module>
    libc backtrace (26 frames, most recent call last):
      27  ???                                 0x0000000000000003 0x0 + 3
      26  libdyld.dylib                       0x00007fff624003d5 start + 1
      25  libpython2.7.dylib                  0x0000000109dd5492 Py_Main + 3490
      24  libpython2.7.dylib                  0x0000000109dbe610 PyRun_SimpleFileExFlags + 816
      23  libpython2.7.dylib                  0x0000000109dbeacd PyRun_FileExFlags + 157
      22  libpython2.7.dylib                  0x0000000109d91282 PyEval_EvalCode + 34
      21  libpython2.7.dylib                  0x0000000109d91b04 PyEval_EvalCodeEx + 2164
      20  libpython2.7.dylib                  0x0000000109d971c9 PyEval_EvalFrameEx + 21609
      19  libpython2.7.dylib                  0x0000000109d9be4d fast_function + 109
      18  libpython2.7.dylib                  0x0000000109d91b04 PyEval_EvalCodeEx + 2164
      17  libpython2.7.dylib                  0x0000000109d971c9 PyEval_EvalFrameEx + 21609
      16  libpython2.7.dylib                  0x0000000109d9be4d fast_function + 109
      15  libpython2.7.dylib                  0x0000000109d91b04 PyEval_EvalCodeEx + 2164
      14  libpython2.7.dylib                  0x0000000109d971c9 PyEval_EvalFrameEx + 21609
      13  libpython2.7.dylib                  0x0000000109d9be4d fast_function + 109
      12  libpython2.7.dylib                  0x0000000109d91b04 PyEval_EvalCodeEx + 2164
      11  libpython2.7.dylib                  0x0000000109d973a8 PyEval_EvalFrameEx + 22088
      10  libpython2.7.dylib                  0x0000000109ceae95 PyObject_Call + 101
      9   libboost_python.dylib               0x000000010aae51d1 boost::python::objects::function_call(_object*, _object*, _object*) + 81
      8   libboost_python.dylib               0x000000010aaeaf28 boost::python::handle_exception_impl(boost::function0<void>) + 72
      7   libboost_python.dylib               0x000000010aae56ca boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) + 26
      6   libboost_python.dylib               0x000000010aae2dc9 boost::python::objects::function::call(_object*, _object*) const + 681
      5   scitbx_math_ext.so                  0x00000001101ff4e7 boost::python::detail::caller_arity<2u>::impl<double (*)(double const&, unsigned int), boost::python::default_call_policies, boost::mpl::vector3<double, double const&, unsigned int> >::operator()(_object*, _object*) + 167
      4   libpython2.7.dylib                  0x0000000109d45e28 tupledealloc + 24
      3   libsystem_platform.dylib            0x00007fff625ebb5d _sigtramp + 29
      2   boost_python_meta_ext.so            0x000000010aa96c20 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):
                    This will NOT solve the problem, just mask it, but
                    may allow you to proceed in case it is not critical.

Which is familiar to me, but no idea if on someone’s to-do list to fix

Basic scitbx math failures seems like a nasty thing to me… but I also know the boost errors are raised very easily…

Cheers Graeme

> On 29 Jul 2019, at 14:50, richard.gildea at diamond.ac.uk wrote:
> Hi,
> Whilst looking into test failures reported against a pull request I currently have open, I noticed that there are several (9) failing tests on the Python 3 build. It appears that Markus reported these 3 weeks ago - is anyone looking into these failures? Having builds permanently reporting failure isn't particularly helpful as it discourages people from looking at the results, and will likely lead to further Python 3 regressions being introduced into the codebase.
> https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=240
> https://github.com/cctbx/cctbx_project/issues
> Cheers,
> Richard
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
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