Comments (19)
Anthchirp
commented on August 30, 2024
clarification: you used python bootstrap.py --builder=dials hot update base build --use-conda, right?
from dxtbx.
ndevenish
commented on August 30, 2024
So I think these lines were changed by me recently? I went through and fixed a load of deprecation warnings because these used to be fromstring, and thought the commands were exactly equivalent; obviously this case was not tested in any test on the deployment I was using
from dxtbx.
Anthchirp
commented on August 30, 2024
https://stackoverflow.com/a/22237279
from dxtbx.
Anthchirp
commented on August 30, 2024
if flex.double() makes a new copy then I would also have thought the outcome to be identical...
from dxtbx.
ndevenish
commented on August 30, 2024
Ah, that makes sense. So we'd need to copy explicitly, perhaps, because fromstring was making deprecation noises.
from dxtbx.
ndevenish
commented on August 30, 2024
if
flex.double()makes a new copy then I would also have thought the outcome to be identical...
I was assuming something something garbage disposal was the problem, but actually it does look like the references should be held. Could be the (old) numpy conversion isn't handling reference counting properly
from dxtbx.
dagewa
commented on August 30, 2024
clarification: you used
python bootstrap.py --builder=dials hot update base build --use-conda, right?
python bootstrap.py --builder=dials base hot update build --use-conda
( [[ -d miniconda3 ]] && source miniconda3/etc/profile.d/conda.sh; conda activate conda_base/ && conda install -y 'qt=4' 'pyqt=4' 'python=2'; )from dxtbx.
dagewa
commented on August 30, 2024
I found that trying to make a flex.double with the first 24 elements of the numpy array succeeded, but using the first 25 elements failed.
from dxtbx.
dagewa
commented on August 30, 2024
In [1]: a1=numpy.frombuffer(array_string, numpy.float)[0:25]
In [2]: a1
Out[2]:
array([40., 3., 40., 16., 23., 0., 4., 65., 0., 2., 6., 20., 32.,
31., 8., 20., 1., -3., -3., -6., 20., 39., 5., 14., 8.])
In [3]: flex.double(a1)
show_stack(1): <ipython-input-3-a4484be0ca88>(1) <module>
show_stack(2): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2878) run_code
show_stack(3): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2824) run_ast_nodes
show_stack(4): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2714) run_cell
show_stack(5): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/interactiveshell.py(486) interact
show_stack(6): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(323) mainloop
show_stack(7): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(228) __call__
show_stack(8): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(385) embed
show_stack(9): /home/fcx32934/sw/cctbx/modules/dials/util/__init__.py(28) debug_console
show_stack(10): /home/fcx32934/sw/cctbx/modules/dxtbx/format/FormatCBFMultiTileHierarchy.py(351) get_raw_data
show_stack(11): /home/fcx32934/sw/cctbx/modules/dxtbx/format/Format.py(94) read
show_stack(12): /home/fcx32934/sw/cctbx/modules/dials/util/masking.py(157) generate
show_stack(13): /home/fcx32934/sw/cctbx/modules/dials/algorithms/spot_finding/finder.py(813) _find_spots_in_imageset
show_stack(14): /home/fcx32934/sw/cctbx/modules/dials/algorithms/spot_finding/finder.py(770) __call__
show_stack(15): /home/fcx32934/sw/cctbx/modules/dials/array_family/flex.py(210) from_observations
show_stack(16): /home/fcx32934/sw/cctbx/build/../modules/dials/command_line/find_spots.py(153) run
show_stack(17): /home/fcx32934/sw/cctbx/build/../modules/dials/command_line/find_spots.py(222) <module>
libc backtrace (84 frames, most recent call last):
/home/fcx32934/sw/cctbx/build/../conda_base/bin/python2.7(+0x107f) [0x55b4aee8807f]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fb98372ab97]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(Py_Main+0xbac) [0x7fb98461816c]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe8) [0x7fb984605f48]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0x78) [0x7fb984604d28]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x100bad) [0x7fb984603bad]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fb9845ea8ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4a84) [0x7fb9845a7a84]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x7047a) [0x7fb98457347a]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x287d9) [0x7fb981e807d9]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x73) [0x7fb981e8bc33]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x2b8f8) [0x7fb981e838f8]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x546) [0x7fb981e83496]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::tuple (*)(dxtbx::ImageSet&, unsigned long), boost::python::default_call_policies, boost::mpl::vector3<boost::python::tuple, dxtbx::ImageSet&, unsigned long> > >::operator()(_object*, _object*)+0x96) [0x7fb979ebfbc6]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::boost_python::ImageSet_get_raw_data(dxtbx::ImageSet&, unsigned long)+0x3b) [0x7fb979eb57bb]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::ImageSet::get_raw_data(unsigned long)+0x64) [0x7fb979ee7fb4]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::ImageSetData::get_data(unsigned long)+0x9e) [0x7fb979ee7aee]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallFunction+0xb3) [0x7fb9846012e3]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fb9845e0c38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x7047a) [0x7fb98457347a]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4a84) [0x7fb9845a7a84]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x70567) [0x7fb984573567]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5b30) [0x7fb9845e6cc0]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fb9845ea8ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa101b) [0x7fb9845a401b]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4764) [0x7fb9845a7764]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x287d9) [0x7fb981e807d9]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x73) [0x7fb981e8bc33]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x2b8f8) [0x7fb981e838f8]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x546) [0x7fb981e83496]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(boost::python::objects::signature_py_function_impl<boost::python::detail::caller<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >* (*)(boost::python::numeric::array const&), boost::python::detail::constructor_policy<boost::python::default_call_policies>, boost::mpl::vector2<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&> >, boost::mpl::v_item<void, boost::mpl::v_item<boost::python::api::object, boost::mpl::v_mask<boost::mpl::vector2<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&>, 1>, 1>, 1> >::operator()(_object*, _object*)+0x4e) [0x7fb98109dd5e]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::boost_python::flex_double_from_numpy_array(boost::python::numeric::array const&)+0x31) [0x7fb9812747c1]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > scitbx::af::boost_python::versa_flex_from_numpy_array<double>(boost::python::numeric::array const&)+0x325f) [0x7fb98129156f]
/lib/x86_64-linux-gnu/libc.so.6(+0x3ef20) [0x7fb983747f20]
/home/fcx32934/sw/cctbx/build/lib/boost_python_meta_ext.so(boost_adaptbx_bus_error_backtrace+0) [0x7fb9820bd970]
Segmentation fault (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.
from dxtbx.
phyy-nx
commented on August 30, 2024
(sending to whole list)
Hi David, can you try this:
libtbx.python -c "import boost.python; import numpy"
Something I saw recently that may be related.
…On Wed, May 15, 2019 at 4:10 AM David Waterman ***@***.***> wrote:
In [1]: a1=numpy.frombuffer(array_string, numpy.float)[0:25]
In [2]: a1
Out[2]:
array([40., 3., 40., 16., 23., 0., 4., 65., 0., 2., 6., 20., 32.,
31., 8., 20., 1., -3., -3., -6., 20., 39., 5., 14., 8.])
In [3]: flex.double(a1)
show_stack(1): <ipython-input-3-a4484be0ca88>(1) <module>
show_stack(2): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2878) run_code
show_stack(3): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2824) run_ast_nodes
show_stack(4): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/core/interactiveshell.py(2714) run_cell
show_stack(5): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/interactiveshell.py(486) interact
show_stack(6): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(323) mainloop
show_stack(7): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(228) __call__
show_stack(8): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/IPython/terminal/embed.py(385) embed
show_stack(9): /home/fcx32934/sw/cctbx/modules/dials/util/__init__.py(28) debug_console
show_stack(10): /home/fcx32934/sw/cctbx/modules/dxtbx/format/FormatCBFMultiTileHierarchy.py(351) get_raw_data
show_stack(11): /home/fcx32934/sw/cctbx/modules/dxtbx/format/Format.py(94) read
show_stack(12): /home/fcx32934/sw/cctbx/modules/dials/util/masking.py(157) generate
show_stack(13): /home/fcx32934/sw/cctbx/modules/dials/algorithms/spot_finding/finder.py(813) _find_spots_in_imageset
show_stack(14): /home/fcx32934/sw/cctbx/modules/dials/algorithms/spot_finding/finder.py(770) __call__
show_stack(15): /home/fcx32934/sw/cctbx/modules/dials/array_family/flex.py(210) from_observations
show_stack(16): /home/fcx32934/sw/cctbx/build/../modules/dials/command_line/find_spots.py(153) run
show_stack(17): /home/fcx32934/sw/cctbx/build/../modules/dials/command_line/find_spots.py(222) <module>
libc backtrace (84 frames, most recent call last):
/home/fcx32934/sw/cctbx/build/../conda_base/bin/python2.7(+0x107f) [0x55b4aee8807f]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fb98372ab97]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(Py_Main+0xbac) [0x7fb98461816c]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xe8) [0x7fb984605f48]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0x78) [0x7fb984604d28]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x100bad) [0x7fb984603bad]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fb9845ea8ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4a84) [0x7fb9845a7a84]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x7047a) [0x7fb98457347a]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x287d9) [0x7fb981e807d9]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x73) [0x7fb981e8bc33]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x2b8f8) [0x7fb981e838f8]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x546) [0x7fb981e83496]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::tuple (*)(dxtbx::ImageSet&, unsigned long), boost::python::default_call_policies, boost::mpl::vector3<boost::python::tuple, dxtbx::ImageSet&, unsigned long> > >::operator()(_object*, _object*)+0x96) [0x7fb979ebfbc6]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::boost_python::ImageSet_get_raw_data(dxtbx::ImageSet&, unsigned long)+0x3b) [0x7fb979eb57bb]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::ImageSet::get_raw_data(unsigned long)+0x64) [0x7fb979ee7fb4]
/home/fcx32934/sw/cctbx/build/lib/dxtbx_imageset_ext.so(dxtbx::ImageSetData::get_data(unsigned long)+0x9e) [0x7fb979ee7aee]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallFunction+0xb3) [0x7fb9846012e3]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fb9845e0c38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x7047a) [0x7fb98457347a]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4a84) [0x7fb9845a7a84]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x70567) [0x7fb984573567]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6a08) [0x7fb9845e7b98]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5b30) [0x7fb9845e6cc0]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fb9845ea8ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fb9845ea6c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3bb9) [0x7fb9845e4d49]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa101b) [0x7fb9845a401b]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xa4764) [0x7fb9845a7764]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x5a80d) [0x7fb98455d80d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fb98454e973]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x287d9) [0x7fb981e807d9]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x73) [0x7fb981e8bc33]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(+0x2b8f8) [0x7fb981e838f8]
/home/fcx32934/sw/cctbx/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x546) [0x7fb981e83496]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(boost::python::objects::signature_py_function_impl<boost::python::detail::caller<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >* (*)(boost::python::numeric::array const&), boost::python::detail::constructor_policy<boost::python::default_call_policies>, boost::mpl::vector2<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&> >, boost::mpl::v_item<void, boost::mpl::v_item<boost::python::api::object, boost::mpl::v_mask<boost::mpl::vector2<scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&>, 1>, 1>, 1> >::operator()(_object*, _object*)+0x4e) [0x7fb98109dd5e]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::boost_python::flex_double_from_numpy_array(boost::python::numeric::array const&)+0x31) [0x7fb9812747c1]
/home/fcx32934/sw/cctbx/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::versa<double, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > scitbx::af::boost_python::versa_flex_from_numpy_array<double>(boost::python::numeric::array const&)+0x325f) [0x7fb98129156f]
/lib/x86_64-linux-gnu/libc.so.6(+0x3ef20) [0x7fb983747f20]
/home/fcx32934/sw/cctbx/build/lib/boost_python_meta_ext.so(boost_adaptbx_bus_error_backtrace+0) [0x7fb9820bd970]
Segmentation fault (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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from dxtbx.
dagewa
commented on August 30, 2024
Hi @phyy-nx, enjoy my stack trace ;-)
fcx32934@zdar:~$ libtbx.python -c "import boost.python; import numpy"
show_stack(1): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/core/getlimits.py(169) <module>
show_stack(2): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/core/__init__.py(51) <module>
show_stack(3): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/lib/type_check.py(11) <module>
show_stack(4): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/lib/__init__.py(8) <module>
show_stack(5): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/add_newdocs.py(13) <module>
show_stack(6): /home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/__init__.py(142) <module>
show_stack(7): <string>(1) <module>
libc backtrace (83 frames, most recent call last):
/home/fcx32934/sw/cctbx/build/../conda_base/bin/python2.7(+0x107f) [0x55dcdcdd807f]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fed553c9b97]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(Py_Main+0x9b2) [0x7fed562b6f72]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleStringFlags+0x3e) [0x7fed562a52ce]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyRun_StringFlags+0x66) [0x7fed562a39c6]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x100bad) [0x7fed562a2bad]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc) [0x7fed5629ae8c]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8578) [0x7fed5629a578]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8b1f) [0x7fed5629ab1f]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x18d) [0x7fed5629af5d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8899) [0x7fed5629a899]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc) [0x7fed5629aecc]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8578) [0x7fed5629a578]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8b1f) [0x7fed5629ab1f]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xbc) [0x7fed5629ae8c]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8578) [0x7fed5629a578]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0xfc) [0x7fed5629aecc]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8578) [0x7fed5629a578]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8b1f) [0x7fed5629ab1f]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x54a8) [0x7fed56285638]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x48) [0x7fed5627fc38]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fed561ed973]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xdc006) [0x7fed5627e006]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x18d) [0x7fed5629af5d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8899) [0x7fed5629a899]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf8323) [0x7fed5629a323]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0xf769d) [0x7fed5629969d]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xae) [0x7fed5629941e]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x1a) [0x7fed562898ea]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7e9) [0x7fed562896c9]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x186e) [0x7fed562819fe]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(PyNumber_Multiply+0x1a) [0x7fed561ebd2a]
/home/fcx32934/sw/cctbx/conda_base/bin/../lib/libpython2.7.so.1.0(+0x4774d) [0x7fed561e974d]
/home/fcx32934/sw/cctbx/conda_base/lib/python2.7/site-packages/numpy/core/umath.so(+0x10edeb) [0x7fed51844deb]
/lib/x86_64-linux-gnu/libc.so.6(+0x3ef20) [0x7fed553e6f20]
/home/fcx32934/sw/cctbx/build/lib/boost_python_meta_ext.so(initboost_python_meta_ext+0) [0x7fed5404c990]
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.
from dxtbx.
Anthchirp
commented on August 30, 2024
https://github.com/numpy/numpy/blob/maintenance/1.15.x/numpy/core/getlimits.py#L169
Suggest CPU to blame?
How about if you apply cctbx/cctbx_project#324?
from dxtbx.
phyy-nx
commented on August 30, 2024
@Anthchirp since the import order doesn't fix it I doubt disabling the fpe traps will either, but it's worth a shot.
In the meantime @dagewa, these two images fail with your patch but work in the master:
dials_regression/image_examples/LCLS_cspad_nexus/idx-20130301060858401.cbf
dials_regression/stills_test_data/hit-20111202210224984.cbf
There are lots of ways to pack cbfs. These are all cspad cbfs I created at different points along the evolution of the format so I'm not surprised some of them are created differently.
from dxtbx.
phyy-nx
commented on August 30, 2024
Indeed, stills_test_data/hit-20111202210224984.cbf and image_examples/LCLS_cspad_nexus/idx-20130301060858401.cbf are signed 32-bit integer but spotfinding_test_data/idx-s00-20131106040302615.cbf is signed 64-bit real IEEE.
from dxtbx.
dagewa
commented on August 30, 2024
Ah ok, I'll try with these images
from dxtbx.
dagewa
commented on August 30, 2024
On https://github.com/cctbx/cctbx_project/tree/invert_boost_signal_default I get
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------
Segmentation fault (core dumped)
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phyy-nx
commented on August 30, 2024
Yah, I kinda expected that
…On Wed, May 15, 2019 at 10:28 AM David Waterman ***@***.***> wrote:
On https://github.com/cctbx/cctbx_project/tree/invert_boost_signal_default
I get
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------
Segmentation fault (core dumped)
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dagewa
commented on August 30, 2024
I think I just got the wrong format string. I pushed a fix
from dxtbx.
phyy-nx
commented on August 30, 2024
Ok looks good. Feel free to merge.
from dxtbx.
Related Issues (20)
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