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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good morning Nigel,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Markus<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></a></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Nigel Moriarty<br>
<b>Sent:</b> 11 April 2015 00:39<br>
<b>To:</b> cctbx mailing list; Paul Adams; Aaron Brewster<br>
<b>Subject:</b> Re: [cctbxbb] scitbx test crashing on mac<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Markus<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">I have been working on changing bootstrap.py but not sure the best way forward.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<div>
<p class="MsoNormal">Cheers<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Nigel<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">---<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : <a href="tel:510-486-5709" target="_blank">510-486-5709</a> Email : <a href="mailto:NWMoriarty@LBL.gov">
NWMoriarty@LBL.gov</a><br>
Fax : <a href="tel:510-486-5909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">
CCI.LBL.gov</a><o:p></o:p></p>
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</div>
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</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Fri, Apr 10, 2015 at 12:46 AM, <<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p>Good morning,<o:p></o:p></p>
<p>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.<o:p></o:p></p>
<p>Apologies if this is not the right place to report scitbx problems to.<o:p></o:p></p>
<p>-Markus<o:p></o:p></p>
<p> <o:p></o:p></p>
<h3>Stacktrace<o:p></o:p></h3>
<pre> 11 Python 0x0000000100010d03 PyObject_Call + 99<o:p></o:p></pre>
<pre> 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83<o:p></o:p></pre>
<pre> 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 7 libboost_python.dylib 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 4 ??? 0x000000010183fc20 0x0 + 4320394272<o:p></o:p></pre>
<pre> 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26<o:p></o:p></pre>
<pre> 2 boost_python_meta_ext.so 0x00000001005bdf80 initboost_python_meta_ext + 0<o:p></o:p></pre>
<pre>Floating-point error (Python and libc call stacks above)<o:p></o:p></pre>
<pre> This crash may be due to a problem in any imported<o:p></o:p></pre>
<pre> Python module, including modules which are not part<o:p></o:p></pre>
<pre> of the cctbx project. To disable the traps leading<o:p></o:p></pre>
<pre> to this message, define these environment variables<o:p></o:p></pre>
<pre> (e.g. assign the value 1):<o:p></o:p></pre>
<pre> BOOST_ADAPTBX_FPE_DEFAULT<o:p></o:p></pre>
<pre> BOOST_ADAPTBX_SIGNALS_DEFAULT<o:p></o:p></pre>
<pre> This will NOT solve the problem, just mask it, but<o:p></o:p></pre>
<pre> may allow you to proceed in case it is not critical.<o:p></o:p></pre>
<h3>Standard Error<o:p></o:p></h3>
<pre>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<o:p></o:p></pre>
<pre>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<o:p></o:p></pre>
<pre>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<o:p></o:p></pre>
<pre>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__<o:p></o:p></pre>
<pre>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<o:p></o:p></pre>
<pre>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<o:p></o:p></pre>
<pre>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><o:p></o:p></pre>
<pre>libc backtrace (43 frames, most recent call last):<o:p></o:p></pre>
<pre> <span lang="DE">44 ??? 0x0000000000000003 0x0 + 3</span><o:p></o:p></pre>
<pre><span lang="DE"> 43 Python 0x0000000100000d71 Python + 3441</span><o:p></o:p></pre>
<pre><span lang="DE"> 42 Python 0x0000000100000e58 Python + 3672</span><o:p></o:p></pre>
<pre><span lang="DE"> </span>41 Python 0x00000001000edd44 Py_Main + 3076<o:p></o:p></pre>
<pre> 40 Python 0x00000001000d64a7 PyRun_SimpleFileExFlags + 711<o:p></o:p></pre>
<pre> 39 Python 0x00000001000d6984 PyRun_FileExFlags + 164<o:p></o:p></pre>
<pre> 38 Python 0x00000001000ad596 PyEval_EvalCode + 54<o:p></o:p></pre>
<pre> 37 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 36 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111<o:p></o:p></pre>
<pre> 35 Python 0x00000001000b5556 fast_function + 118<o:p></o:p></pre>
<pre> 34 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 33 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111<o:p></o:p></pre>
<pre> 32 Python 0x00000001000b5556 fast_function + 118<o:p></o:p></pre>
<pre> 31 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 30 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651<o:p></o:p></pre>
<pre> 29 Python 0x0000000100010d03 PyObject_Call + 99<o:p></o:p></pre>
<pre> 28 Python 0x0000000100069e23 type_call + 339<o:p></o:p></pre>
<pre> 27 Python 0x000000010006fccd slot_tp_init + 141<o:p></o:p></pre>
<pre> 26 Python 0x0000000100010d03 PyObject_Call + 99<o:p></o:p></pre>
<pre> 25 Python 0x000000010001e207 instancemethod_call + 247<o:p></o:p></pre>
<pre> 24 Python 0x0000000100010d03 PyObject_Call + 99<o:p></o:p></pre>
<pre> 23 Python 0x0000000100036a6c function_call + 364<o:p></o:p></pre>
<pre> 22 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 21 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111<o:p></o:p></pre>
<pre> 20 Python 0x00000001000b5556 fast_function + 118<o:p></o:p></pre>
<pre> 19 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 18 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111<o:p></o:p></pre>
<pre> 17 Python 0x00000001000b5556 fast_function + 118<o:p></o:p></pre>
<pre> 16 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 15 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111<o:p></o:p></pre>
<pre> 14 Python 0x00000001000b5556 fast_function + 118<o:p></o:p></pre>
<pre> 13 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666<o:p></o:p></pre>
<pre> 12 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651<o:p></o:p></pre>
<pre> 11 Python 0x0000000100010d03 PyObject_Call + 99<o:p></o:p></pre>
<pre> 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83<o:p></o:p></pre>
<pre> 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 7 libboost_python.dylib 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 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<o:p></o:p></pre>
<pre> 4 ??? 0x000000010183fc20 0x0 + 4320394272<o:p></o:p></pre>
<pre> 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26<o:p></o:p></pre>
<pre> 2 boost_python_meta_ext.so 0x00000001005bdf80 initboost_python_meta_ext + 0<o:p></o:p></pre>
<pre>Floating-point error (Python and libc call stacks above)<o:p></o:p></pre>
<pre> This crash may be due to a problem in any imported<o:p></o:p></pre>
<pre> Python module, including modules which are not part<o:p></o:p></pre>
<pre> of the cctbx project. To disable the traps leading<o:p></o:p></pre>
<pre> to this message, define these environment variables<o:p></o:p></pre>
<pre> (e.g. assign the value 1):<o:p></o:p></pre>
<pre> BOOST_ADAPTBX_FPE_DEFAULT<o:p></o:p></pre>
<pre> BOOST_ADAPTBX_SIGNALS_DEFAULT<o:p></o:p></pre>
<pre> This will NOT solve the problem, just mask it, but<o:p></o:p></pre>
<pre> may allow you to proceed in case it is not critical.<o:p></o:p></pre>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> <o:p></o:p></span></p>
</div>
<p><span style="color:#888888"> <o:p></o:p></span></p>
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