Re: [matplotlib-devel] weird error with gcc 4.4, gomp, cython, and matplotlib
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= 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 -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] weird error with gcc 4.4, gomp, cython, and matplotlib
On Thu, Jan 28, 2010 at 2:00 AM, Robert Bradshaw 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/ + hoy...@gmail.com ++ -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
[matplotlib-devel] zorder for contours
Hi, I was shown a bug today by a colleague, demonstrated by the following example: import numpy as np import matplotlib.pyplot as plt a = np.zeros([10, 10]) a[2:6,3:8] = 1 ls = plt.contour(a, 1, colors='r', linewidths=3, zorder=5) print ls.collections[0]l.get_zorder() rect = plt.Rectangle([2, 3], 5, 4, zorder=3) plt.gca().add_artist(rect) plt.show() Unless I completely misunderstand zorder, the contour should be *on top* of the rectangle. Also note that printing the zorder for the contour's collection (a LineCollection object) gives a value of 2, even though the call to contour() specified 5 for the zorder. Looking over the code for contour, the zorder is never mentioned. The reason the LineCollection ends up with a value of 2 is that this is the default for a LineCollection. My question is: is there any reason *not* to use the passed in zorder for contours/filled contours? If this is the proper fix, I'll check it in myself, I just wanted to make sure I'm not missing some special case here. As an aside, this is yet another example where it would be nice to know that a keyword argument was not being used. If there's no objections, I'd be willing to change ContourSet to pop arguments off of **kwargs so that it can see if some aren't used and throw an exception if not all are used. On the other hand, this could break existing code that are passing extra/useless kwargs, so maybe a warning would be better? Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] zorder for contours
Ryan May wrote: > Hi, > > I was shown a bug today by a colleague, demonstrated by the following example: > > import numpy as np > import matplotlib.pyplot as plt > > a = np.zeros([10, 10]) > a[2:6,3:8] = 1 > ls = plt.contour(a, 1, colors='r', linewidths=3, zorder=5) > print ls.collections[0]l.get_zorder() > rect = plt.Rectangle([2, 3], 5, 4, zorder=3) > plt.gca().add_artist(rect) > plt.show() > > Unless I completely misunderstand zorder, the contour should be *on > top* of the rectangle. Also note that printing the zorder for the > contour's collection (a LineCollection object) gives a value of 2, > even though the call to contour() specified 5 for the zorder. Looking > over the code for contour, the zorder is never mentioned. The reason > the LineCollection ends up with a value of 2 is that this is the > default for a LineCollection. My question is: is there any reason > *not* to use the passed in zorder for contours/filled contours? If > this is the proper fix, I'll check it in myself, I just wanted to make > sure I'm not missing some special case here. Ryan, Certainly it makes sense to support zorder in some fashion, and the simple way is as you suggest, with one value per call to contour. It may be best to stop there--but I can imagine the next complaint being, "why doesn't zorder support a sequence?", and then things get quite a bit more complicated. Anyway, go ahead and put in the simple zorder support; I don't see any downside to it. > > As an aside, this is yet another example where it would be nice to > know that a keyword argument was not being used. If there's no > objections, I'd be willing to change ContourSet to pop arguments off > of **kwargs so that it can see if some aren't used and throw an > exception if not all are used. On the other hand, this could break > existing code that are passing extra/useless kwargs, so maybe a > warning would be better? Careful. Keeping track of which kwargs are used, and making sure they are always popped, and don't need to remain in the kwargs dictionary, could get tricky. I just added support for the units-related kwargs. I think what you suggest will work, and I agree that some error-trapping for kwarg accidents (misspelling kwargs, or otherwise trying to use a kwarg that has no effect) is a good idea. This sounds like an area where some general mpl coding guidelines, and quite a bit of work to implement them, would be good. Eric > > Ryan > -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] zorder for contours
On Thu, Jan 28, 2010 at 1:03 PM, Eric Firing wrote: > Ryan May wrote: >> Unless I completely misunderstand zorder, the contour should be *on >> top* of the rectangle. Also note that printing the zorder for the >> contour's collection (a LineCollection object) gives a value of 2, >> even though the call to contour() specified 5 for the zorder. Looking >> over the code for contour, the zorder is never mentioned. The reason >> the LineCollection ends up with a value of 2 is that this is the >> default for a LineCollection. My question is: is there any reason >> *not* to use the passed in zorder for contours/filled contours? If >> this is the proper fix, I'll check it in myself, I just wanted to make >> sure I'm not missing some special case here. > > Ryan, > > Certainly it makes sense to support zorder in some fashion, and the simple > way is as you suggest, with one value per call to contour. It may be best > to stop there--but I can imagine the next complaint being, "why doesn't > zorder support a sequence?", and then things get quite a bit more > complicated. > > Anyway, go ahead and put in the simple zorder support; I don't see any > downside to it. Will do shortly. >> As an aside, this is yet another example where it would be nice to >> know that a keyword argument was not being used. If there's no >> objections, I'd be willing to change ContourSet to pop arguments off >> of **kwargs so that it can see if some aren't used and throw an >> exception if not all are used. On the other hand, this could break >> existing code that are passing extra/useless kwargs, so maybe a >> warning would be better? > > Careful. Keeping track of which kwargs are used, and making sure they are > always popped, and don't need to remain in the kwargs dictionary, could get > tricky. I just added support for the units-related kwargs. I think what > you suggest will work, and I agree that some error-trapping for kwarg > accidents (misspelling kwargs, or otherwise trying to use a kwarg that has > no effect) is a good idea. > > This sounds like an area where some general mpl coding guidelines, and quite > a bit of work to implement them, would be good. Agreed. After I wrote this, I thought about it some more, and it's not something you can really do piecemeal due to passing off to base classes and what not. It's a big usability wart however, like when accidentally using 'linewidth' instead of 'linewidths' for calling contour. I'll just leave this as a future improvement. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma Sent from Norman, Oklahoma, United States -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] A small improvement to plot directive
On Wed, Jan 27, 2010 at 6:06 PM, Andrew Straw wrote: > I'm +1 on this. We can have then have the buildbot doc builder enable > this when building the docs. (Which are output at > http://matplotlib.sourceforge.net/trunk-docs/ and > http://matplotlib.sourceforge.net/trunk-docs/Matplotlib.pdf , for > reference .) Thanks, with your and John's (off-list) approvals, it's committed. The patch that went in had more docs than what I posted here, but the code is identical. Cheers, f -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
