matplotlib-devel Mailing List for matplotlib

On Sun, Nov 29, 2009 at 9:49 AM, Jouni K. Seppänen <jk...@ik...> wrote:
> Matthew Brett <mat...@gm...>
> writes:
>
>>> Can you get a backtrace in gdb?
>>
>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>> Reason: 13 at address: 0x0000000000000000
>> 0x0000000102d96ffb in py_to_agg_transformation_matrix
>> (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21
>> 21      matrix = (PyArrayObject*) PyArray_FromObject(obj,
>> PyArray_DOUBLE, 2, 2);
>
> Can you type "bt" in gdb at this point to see the whole call stack?
Sorry - yes - here:
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: 13 at address: 0x0000000000000000
0x0000000102cf703b in py_to_agg_transformation_matrix
(obj=0x102cde590, errors=false) at src/agg_py_transforms.cpp:21
21	 matrix = (PyArrayObject*) PyArray_FromObject(obj,
PyArray_DOUBLE, 2, 2);
(gdb) bt
#0 0x0000000102cf703b in py_to_agg_transformation_matrix
(obj=0x102cde590, errors=false) at src/agg_py_transforms.cpp:21
#1 0x0000000102cf762c in get_path_iterator (path=0x102cde710,
trans=<value temporarily unavailable, due to optimizations>,
remove_nans=1, do_clip=0, rect=0x7fff5fbf9480,
quantize_mode=QUANTIZE_AUTO, do_simplify=1) at src/path_cleanup.cpp:58
#2 0x0000000102ce9e90 in GraphicsContext_draw_path (self=0x102cd19d0,
args=<value temporarily unavailable, due to optimizations>) at
src/_macosx.m:881
#3 0x00000001000b31d8 in PyEval_EvalFrameEx (f=0x102b65f50,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3706
#4 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cd0be8,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102b61900, argcount=5, kws=0x102b61928, kwcount=0,
defs=0x102cde1a8, defcount=1, closure=0x0) at Python/ceval.c:2968
#5 0x00000001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#6 0x00000001000b1f1d in PyEval_EvalFrameEx (f=0x102b61720,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3727
#7 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x10180ceb8,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102cae2a8, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#8 0x00000001000362a5 in function_call (func=0x101839b18,
arg=0x102cae290, kw=0x0) at Objects/funcobject.c:524
#9 0x0000000100006fe2 in PyObject_Call (func=0x101839b18,
arg=0x102cae290, kw=0x0) at Objects/abstract.c:2492
#10 0x00000001000ae352 in PyEval_EvalFrameEx (f=0x102b61530,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:4019
#11 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x1014647b0,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102b61100, argcount=2, kws=0x102b61110, kwcount=0, defs=0x0,
defcount=0, closure=0x101825dc0) at Python/ceval.c:2968
#12 0x00000001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#13 0x00000001000b1f1d in PyEval_EvalFrameEx (f=0x102b60f00,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3727
#14 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102c90288,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102cae260, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#15 0x00000001000362a5 in function_call (func=0x102cad1b8,
arg=0x102cae248, kw=0x0) at Objects/funcobject.c:524
#16 0x0000000100006fe2 in PyObject_Call (func=0x102cad1b8,
arg=0x102cae248, kw=0x0) at Objects/abstract.c:2492
#17 0x00000001000ae352 in PyEval_EvalFrameEx (f=0x102b607f0,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:4019
#18 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x1014647b0,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102cae218, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x102c8d6e0) at Python/ceval.c:2968
#19 0x00000001000362a5 in function_call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/funcobject.c:524
#20 0x0000000100006fe2 in PyObject_Call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/abstract.c:2492
#21 0x000000010001905d in instancemethod_call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/classobject.c:2579
#22 0x0000000100006fe2 in PyObject_Call (func=0x102aa7fa0,
arg=0x100438c90, kw=0x0) at Objects/abstract.c:2492
#23 0x000000010000a760 in call_function_tail [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Objects/abstract.c:2524
#24 0x000000010000a760 in PyObject_CallMethod (o=<value temporarily
unavailable, due to optimizations>, name=<value temporarily
unavailable, due to optimizations>, format=0x102cfd504 "O") at
Objects/abstract.c:2601
#25 0x0000000102ce5653 in -[View drawRect:] (self=0x102b50960,
_cmd=<value temporarily unavailable, due to optimizations>,
rect={origin = {x = 0, y = 0}, size = {width = 640, height = 480}}) at
src/_macosx.m:4517
#26 0x00007fff8676afae in -[NSView _drawRect:clip:] ()
#27 0x00007fff86769c21 in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#28 0x00007fff86769f8b in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#29 0x00007fff86769f8b in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#30 0x00007fff867682f3 in -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
()
#31 0x00007fff86767e17 in -[NSThemeFrame
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
()
#32 0x00007fff867646bf in -[NSView
_displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:]
()
#33 0x00007fff866ddf37 in -[NSView displayIfNeeded] ()
#34 0x00007fff866a5f87 in -[NSWindow
_reallyDoOrderWindow:relativeTo:findKey:forCounter:force:isModal:] ()
#35 0x00007fff866a5b1c in -[NSWindow orderWindow:relativeTo:] ()
#36 0x00007fff866a349e in -[NSWindow makeKeyAndOrderFront:] ()
#37 0x0000000102ce490e in FigureManager_init (self=0x102d30908,
args=<value temporarily unavailable, due to optimizations>,
kwds=<value temporarily unavailable, due to optimizations>) at
src/_macosx.m:3338
#38 0x000000010006533c in wrap_init (self=<value temporarily
unavailable, due to optimizations>, args=<value temporarily
unavailable, due to optimizations>, wrapped=<value temporarily
unavailable, due to optimizations>, kwds=<value temporarily
unavailable, due to optimizations>) at Objects/typeobject.c:4694
#39 0x0000000100006fe2 in PyObject_Call (func=0x102cde6d0,
arg=0x102cae1b8, kw=0x0) at Objects/abstract.c:2492
#40 0x00000001000ab047 in PyEval_CallObjectWithKeywords
(func=0x102cde6d0, arg=0x102cae1b8, kw=0x0) at Python/ceval.c:3575
#41 0x0000000100024164 in wrapperdescr_call (descr=<value temporarily
unavailable, due to optimizations>, args=0x102cae1b8, kwds=0x0) at
Objects/descrobject.c:304
#42 0x0000000100006fe2 in PyObject_Call (func=0x102cbecd0,
arg=0x102c72b40, kw=0x0) at Objects/abstract.c:2492
#43 0x00000001000af47e in do_call [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3924
#44 0x00000001000af47e in call_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3729
#45 0x00000001000af47e in PyEval_EvalFrameEx (f=0x102b56400,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:2389
#46 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cd5f30,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x3, argcount=3, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:2968
#47 0x00000001000362a5 in function_call (func=0x102cdfc80,
arg=0x1002a4910, kw=0x0) at Objects/funcobject.c:524
#48 0x0000000100006fe2 in PyObject_Call (func=0x102cdfc80,
arg=0x1002a4910, kw=0x0) at Objects/abstract.c:2492
#49 0x000000010001905d in instancemethod_call (func=0x102cdfc80,
arg=0x1002a4910, kw=0x0) at Objects/classobject.c:2579
#50 0x0000000100006fe2 in PyObject_Call (func=0x102aa7e60,
arg=0x102c84128, kw=0x0) at Objects/abstract.c:2492
#51 0x000000010006bf18 in slot_tp_init (self=<value temporarily
unavailable, due to optimizations>, args=0x102c84128, kwds=0x0) at
Objects/typeobject.c:5638
#52 0x0000000100068b65 in type_call (type=0x102b44b30,
args=0x102c84128, kwds=0x0) at Objects/typeobject.c:745
#53 0x0000000100006fe2 in PyObject_Call (func=0x102b44b30,
arg=0x102c84128, kw=0x0) at Objects/abstract.c:2492
#54 0x00000001000af47e in do_call [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3924
#55 0x00000001000af47e in call_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3729
#56 0x00000001000af47e in PyEval_EvalFrameEx (f=0x102b3d120,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:2389
#57 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cd5738,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102cce848, argcount=1, kws=0x102b48370, kwcount=6, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#58 0x00000001000363ad in function_call (func=0x102cdf6e0,
arg=0x100421450, kw=0x101526720) at Objects/funcobject.c:524
#59 0x0000000100006fe2 in PyObject_Call (func=0x102cdf6e0,
arg=0x100421450, kw=0x101526720) at Objects/abstract.c:2492
#60 0x00000001000ae352 in PyEval_EvalFrameEx (f=0x101526a60,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:4019
#61 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cb5a08,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x8, argcount=0, kws=0x102b48188, kwcount=0, defs=0x102ccea08,
defcount=7, closure=0x0) at Python/ceval.c:2968
#62 0x00000001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#63 0x00000001000b1f1d in PyEval_EvalFrameEx (f=0x102b48000,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3727
#64 0x00000001000b237a in PyEval_EvalFrameEx (f=0x100357cf0,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3792
#65 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cb84e0,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x10035a950, argcount=0, kws=0x10035a950, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#66 0x00000001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#67 0x00000001000b1f1d in PyEval_EvalFrameEx (f=0x10035a7a0,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3727
#68 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x102cc4738,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x102cc0c30, argcount=2, kws=0x100359160, kwcount=1, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#69 0x00000001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#70 0x00000001000b1f1d in PyEval_EvalFrameEx (f=0x100358fd0,
throwflag=<value temporarily unavailable, due to optimizations>) at
Python/ceval.c:3727
#71 0x00000001000b3f30 in PyEval_EvalCodeEx (co=0x100426f30,
globals=<value temporarily unavailable, due to optimizations>,
locals=<value temporarily unavailable, due to optimizations>,
args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:2968
#72 0x00000001000b4016 in PyEval_EvalCode (co=<value temporarily
unavailable, due to optimizations>, globals=<value temporarily
unavailable, due to optimizations>, locals=<value temporarily
unavailable, due to optimizations>) at Python/ceval.c:522
#73 0x00000001000d8a5e in run_mod [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/pythonrun.c:1335
#74 0x00000001000d8a5e in PyRun_FileExFlags (fp=0x7fff7092be80,
filename=0x7fff5fbfe17a
"scipybuild/matplotlib/examples/pylab_examples/simple_plot.py",
start=<value temporarily unavailable, due to optimizations>,
globals=0x100312ec0, locals=0x100312ec0, closeit=1,
flags=0x7fff5fbfdfb0) at Python/pythonrun.c:1321
#75 0x00000001000d8d19 in PyRun_SimpleFileExFlags (fp=0x7fff7092be80,
filename=0x7fff5fbfe17a
"scipybuild/matplotlib/examples/pylab_examples/simple_plot.py",
closeit=1, flags=0x7fff5fbfdfb0) at Python/pythonrun.c:931
#76 0x00000001000e835c in Py_Main (argc=2523360, argv=0x7fff5fbfe010)
at Modules/main.c:599
#77 0x0000000100001544 in start ()
Current language: auto; currently c++
Mathew

Matthew Brett <mat...@gm...>
writes:
>> Can you get a backtrace in gdb?
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: 13 at address: 0x0000000000000000
> 0x0000000102d96ffb in py_to_agg_transformation_matrix
> (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21
> 21	 matrix = (PyArrayObject*) PyArray_FromObject(obj,
> PyArray_DOUBLE, 2, 2);
Can you type "bt" in gdb at this point to see the whole call stack?
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Hi,
>> Can you get a backtrace in gdb?
>
> (gdb) run scipybuild/matplotlib/examples/pylab_examples/simple_plot.py
...
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: 13 at address: 0x0000000000000000
> 0x0000000102d96ffb in py_to_agg_transformation_matrix
> (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21
> 21       matrix = (PyArrayObject*) PyArray_FromObject(obj,
> PyArray_DOUBLE, 2, 2);
>
> hum... I'm running from the latest svn numpy...
Same outcome with numpy 1.3 though...
Matthew

Hi,
On Sun, Nov 29, 2009 at 1:30 AM, Jouni K. Seppänen <jk...@ik...> wrote:
> Matthew Brett <mat...@gm...> writes:
>
>> I am rashly building matplotlib from source on Snow Leopard, and
>> getting a segmentation fault as soon as I try and do a plot.
>
> Can you get a backtrace in gdb?
(gdb) run scipybuild/matplotlib/examples/pylab_examples/simple_plot.py
...
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: 13 at address: 0x0000000000000000
0x0000000102d96ffb in py_to_agg_transformation_matrix
(obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21
21	 matrix = (PyArrayObject*) PyArray_FromObject(obj,
PyArray_DOUBLE, 2, 2);
hum... I'm running from the latest svn numpy...
Cheers,
Matthew

Matthew Brett <mat...@gm...> writes:
> I am rashly building matplotlib from source on Snow Leopard, and
> getting a segmentation fault as soon as I try and do a plot.
Can you get a backtrace in gdb? 
-- 
Jouni K. Seppänen
http://www.iki.fi/jks

> I am rashly building matplotlib from source on Snow Leopard, and
> getting a segmentation fault as soon as I try and do a plot.
>
> me $ python -c 'import pylab; pylab.plot(range(10))'
> Segmentation fault
Sorry - here the is top of the build output:
export PKG_CONFIG_PATH="/Users/mb312/usr/local/lib/pkgconfig" &&\
	export MACOSX_DEPLOYMENT_TARGET=10.6 &&\
	export CFLAGS=" -I/Users/mb312/usr/local/include
-I/Users/mb312/usr/local/include/freetype2 -isysroot
/Developer/SDKs/MacOSX10.6.sdk" &&\
	export LDFLAGS=" -L/Users/mb312/usr/local/lib
-syslibroot,/Developer/SDKs/MacOSX10.6.sdk" &&\
	python2.6 setup.py install --prefix=/Users/mb312/usr/local
============================================================================
BUILDING MATPLOTLIB
 matplotlib: 1.0.svn
 python: 2.6.4 (r264:75706, Nov 29 2009, 00:03:57) [GCC
 4.2.1 (Apple Inc. build 5646) (dot 1)]
 platform: darwin
REQUIRED DEPENDENCIES
 numpy: 1.4.0.dev7803
 freetype2: found, but unknown version (no pkg-config)
 * WARNING: Could not find 'freetype2' headers in any
 * of '.', './freetype2'.
OPTIONAL BACKEND DEPENDENCIES
 libpng: found, but unknown version (no pkg-config)
 * Could not find 'libpng' headers in any of '.'
 Tkinter: Tkinter: 73770, Tk: 8.5, Tcl: 8.5
 wxPython: no
 * wxPython not found
 Gtk+: no
 * Building for Gtk+ requires pygtk; you must be able
 * to "import gtk" in your build/install environment
 Mac OS X native: yes
 Qt: no
 Qt4: no
 Cairo: no
OPTIONAL DATE/TIMEZONE DEPENDENCIES
 datetime: present, version unknown
 dateutil: matplotlib will provide
 pytz: 2008c
OPTIONAL USETEX DEPENDENCIES
 dvipng: no
 ghostscript: /bin/sh: gs: command not found
 latex: no
Thanks a lot,
Matthew

Hi,
I am rashly building matplotlib from source on Snow Leopard, and
getting a segmentation fault as soon as I try and do a plot.
me $ python -c 'import pylab; pylab.plot(range(10))'
Segmentation fault
I've built python myself with:
export MACOSX_DEPLOYMENT_TARGET=10.6
./configure --prefix=/Users/mb312/usr/local
Then numpy using the usual procedure (tests look good)
For matplotlib, I've hacked the make.osx file so the top looks like:
---- begin make.osx snippet ----
PYVERSION=2.6
PYTHON=python${PYVERSION}
ZLIBVERSION=1.2.3
PNGVERSION=1.2.40
FREETYPEVERSION=2.3.11
MACOSX_DEPLOYMENT_TARGET=10.6
OSX_SDK_VER=10.6
ARCH_FLAGS=
## You shouldn't need to configure past this point
PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig"
CFLAGS="${ARCH_FLAGS} -I${PREFIX}/include
-I${PREFIX}/include/freetype2 -isysroot
/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
LDFLAGS="${ARCH_FLAGS} -L${PREFIX}/lib
-syslibroot,/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
--- end make.osx snippet ---
This builds correctly but then causes the segfault above. I've tried
with the original make.osx package versions of freetype and libpng
with the same outcome.
Running simple_script.py:
blair:~ mb312$ python
scipybuild/matplotlib/examples/pylab_examples/simple_plot.py
--verbose-helpful
$HOME=/Users/mb312
CONFIGDIR=/Users/mb312/.matplotlib
matplotlib data path
/Users/mb312/usr/local/lib/python2.6/site-packages/matplotlib/mpl-data
loaded rc file /Users/mb312/usr/local/lib/python2.6/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 1.0.svn
verbose.level helpful
interactive is False
units is False
platform is darwin
Using fontManager instance from /Users/mb312/.matplotlib/fontList.cache
backend MacOSX version unknown
Segmentation fault
gcc version is i686-apple-darwin10-gcc-4.2.1
Did I take a mis-step somewhere in the build process? Any advice very
gratefully received...
Thanks a lot,
Matthew