Hi All,
I'm trying to track down a sporadic Fatal python error in a
complicated data analysis program I'm writing. Quick explanation: I
have a qt gui that launches a python task-manager thread. That thread
creates a multiprocessing.Pool, and iterates through a list of data in
an hdf5 file, passing each item of data to Pool.apply_async. A
callback takes the result and updates an entry in the hdf5 file, and
appends an item to a queue. The qt gui uses a qtimer to check the
queue once a second. If the queue is not empty, it reads the hdf5 file
and updates an imshow image. I can click a pixel in the image, which
plots the spectrum and fit associated with that pixel. I can then
click a qt button to switch between lin and log scales in the spectrum
plot. If the taskmanager thread is running, changing between lin and
log scales can pretty reliably cause a crash (especially on Fedora
14):
python: /builddir/build/BUILD/Python-2.7/Modules/gcmodule.c:311:
update_refs: Assertion `gc->gc.gc_refs != 0' failed.
Aborted (core dumped)
That's not a lot of information to go on, and I'm drawing on a ton of
extension modules in my program: numpy, h5py, qt, matplotlib, pymca.
We've also been able to get the program to crash on mac:
Exception AttributeError: "'BboxTransformTo' object has no attribute
'data'" in <function remove at 0x128752410> ignored
Traceback (most recent call last):
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py",
line 83, in paintEvent
FigureCanvasAgg.draw(self)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py",
line 394, in draw
self.figure.draw(self.renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py",
line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/figure.py",
line 798, in draw
func(*args)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py",
line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes.py",
line 1946, in draw
a.draw(renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/artist.py",
line 55, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/legend.py",
line 430, in draw
self._legend_box.draw(renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/offsetbox.py",
line 240, in draw
c.draw(renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/offsetbox.py",
line 240, in draw
c.draw(renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/offsetbox.py",
line 240, in draw
c.draw(renderer)
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/offsetbox.py",
line 239, in draw
c.set_offset((px+ox, py+oy))
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/offsetbox.py",
line 460, in set_offset
self.offset_transform.clear()
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/transforms.py",
line 1549, in clear
self.invalidate()
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/transforms.py",
line 124, in invalidate
stack.extend(root._parents.keys())
AttributeError: 'list' object has no attribute 'keys'
Fatal Python error: GC object already tracked
Abort trap
All access to hdf5 is protected with a thread lock, and I have made
some fairly stressful scripts testing h5py/threading/multiprocessing
and haven't been able to produce a crash.
Does anyone have suggestions on how I can try to track down this
problem? These GC reports are not giving me much to go on, how can I
determine to which extension module these objects with bad reference
counts belong?
Thanks, and sorry for the long and obscure post.
Darren
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