I'm really not sure which mailing list to report this on -- it has got to rank up there with one of the most obscure errors of all times. I suspect it's an error in gcc's new openmp implementation, gomp, but not sure; I can report it there if people think I should. In gcc 4.4.1, when I compile a completely empty .pyx module in (1) c++ mode and (2) pass -lgomp to the linker, simply (3) importing that empty module causes any subsequent use of matplotlib to segfault the program. Changing either (1), (2) or (3) makes the error go away. I'm using the latest 32bit ubuntu (9.10), python 2.6.4, with the latest cython-devel (2820:105c661599c9) and the latest matplotlib from svn (8097). In matplotlib, I'm using the qt4agg backend. Everything else appears to be working save for this error. If my main file is simply: import tests.emptymodule import tests.plottest where emptymodules is a completely empty cython module and plottest is from matplotlib.pylab import * figure() plot([0,1], [0,1], '-b') show() The program segfaults on the plot() call, with backtrace (gdb) bt 8 #0 0x00e03bc7 in __cxa_allocate_exception () from /usr/lib/libstdc++.so.6 #1 0x0093f282 in py_to_agg_transformation_matrix (obj=0x8223f58, errors=false) at src/agg_py_transforms.cpp:20 #2 0x00946ff3 in _path_module::update_path_extents (this=0x8856098, args=...) at src/path.cpp:346 #3 0x0094e2fd in Py::ExtensionModule<_path_module>::invoke_method_varargs (this=<value optimized out>, method_def=0x8476e00, args=...) at ./CXX/Python2/ExtensionModule.hxx:184 #4 0x0093ae26 in method_varargs_call_handler (_self_and_name_tuple=0x888448c, _args=0x8f052fc) at CXX/Python2/cxx_extensions.cxx:1714 #5 0x080dc0d0 in PyEval_EvalFrameEx () #6 0x080dddf2 in PyEval_EvalCodeEx () #7 0x080dc1b4 in PyEval_EvalFrameEx () Other commands like imshow also cause a segfault. Anyway, I can get by for now without openmp, but I'm curious if anyone has ideas about this bug. I've attached a tarball with the code that reproduces it for me; simply run build.sh and run. Thanks! -- hoyt ++++++++++++++++++++++++++++++++++++++++++++++++ + Hoyt Koepke + University of Washington Department of Statistics + http://www.stat.washington.edu/~hoytak/ + ho...@gm... ++++++++++++++++++++++++++++++++++++++++++
Hoyt Koepke wrote: > I'm really not sure which mailing list to report this on -- it has got > to rank up there with one of the most obscure errors of all times. I > suspect it's an error in gcc's new openmp implementation, gomp, but > not sure; I can report it there if people think I should. > > In gcc 4.4.1, when I compile a completely empty .pyx module in (1) c++ > mode and (2) pass -lgomp to the linker, simply (3) importing that > empty module causes any subsequent use of matplotlib to segfault the > program. Changing either (1), (2) or (3) makes the error go away. > > I'm using the latest 32bit ubuntu (9.10), python 2.6.4, with the > latest cython-devel (2820:105c661599c9) and the latest matplotlib from > svn (8097). In matplotlib, I'm using the qt4agg backend. Everything > else appears to be working save for this error. > > If my main file is simply: > > import tests.emptymodule > import tests.plottest > > where emptymodules is a completely empty cython module and plottest is > > from matplotlib.pylab import * > > figure() > plot([0,1], [0,1], '-b') > show() > > The program segfaults on the plot() call, with backtrace > > (gdb) bt 8 > #0 0x00e03bc7 in __cxa_allocate_exception () from /usr/lib/libstdc++.so.6 > #1 0x0093f282 in py_to_agg_transformation_matrix (obj=0x8223f58, > errors=false) at src/agg_py_transforms.cpp:20 > #2 0x00946ff3 in _path_module::update_path_extents (this=0x8856098, > args=...) at src/path.cpp:346 > #3 0x0094e2fd in > Py::ExtensionModule<_path_module>::invoke_method_varargs (this=<value > optimized out>, method_def=0x8476e00, args=...) > at ./CXX/Python2/ExtensionModule.hxx:184 > #4 0x0093ae26 in method_varargs_call_handler > (_self_and_name_tuple=0x888448c, _args=0x8f052fc) at > CXX/Python2/cxx_extensions.cxx:1714 > #5 0x080dc0d0 in PyEval_EvalFrameEx () > #6 0x080dddf2 in PyEval_EvalCodeEx () > #7 0x080dc1b4 in PyEval_EvalFrameEx () > > It works for me here, but of course, I have a slightly different system. gcc-4.3, python 2.5.2, Cython 0.12, and matplotlib SVN 8097. Have you verified that the same C++ compiler and version of libstdc++ is being used for everything? Mike -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA
On Thu, Jan 28, 2010 at 2:00 AM, Robert Bradshaw <rob...@ma...> wrote: [snip] > I'm guessing that's the issue, but just to be sure, try using the bare I still get the error with the super-bare extension module, so cython's off the hook :-). > Have you verified that the same C++ compiler and version of libstdc++ is > being used for everything? I've tried it two ways; first with everything -- numpy, scipy, matplotlib -- installed and compiled from svn, and one with them installed from the latest ubuntu repositories. I also tried it on both machines I have access to; a 64bit server with gcc 4.3.3 and python 2.6.2, and a 32bit one with gcc 4.4.1 and python 2.6.4. The error is the same on both of those. The python version and the gcc compiler are the two things in common. > If you did upgrade NumPy, rebuild *everything* of compiled code > which depends on it. Yes I did do that, and recompiled everything, but still good to check. gcc is smelling fishier and fishier (or maybe python 2.6?). -- Hoyt ++++++++++++++++++++++++++++++++++++++++++++++++ + Hoyt Koepke + University of Washington Department of Statistics + http://www.stat.washington.edu/~hoytak/ + ho...@gm... ++++++++++++++++++++++++++++++++++++++++++