Thread: [matplotlib-devel] memory leak: gtk.gdk.Pixbuf and gtk.gdk.GCX11 with gtkagg backend

Hi,

I'm looking for memory leaks in a python application and found leaks in
matplotlib. The application is graphic intensive. Each time it updates
the screen, matplotlib allocates another 5-10 megabytes memory for the
new gtk.gdk.Pixbuf and gtk.gdk.GCX11 while does not free up the buffers
allocated for the previous content.

I switched on garbage collection debugging with:

import gc
gc.enable()
gc.set_debug(gc.DEBUG_LEAK)

and tried to delete the leaking objects:

--- ./lib/matplotlib/backends/backend_gtkagg.py 2008-06-23
04:09:29.000000000 +0200 ++
+ /usr/lib/python2.4/site-packages/matplotlib-0.91.4-py2.4-linux-i686.egg/matplotlib/backends/backend_gtkagg.py
2008-10-02 00:05:32.000000000 +0200 @@ -3,6 +3,7 @@ """
 from __future__ import division
 import os
+import gc

 import matplotlib
 from matplotlib.figure import Figure
@@ -82,8 +83,17 @@
         h = int(ren.height)
         pixbuf = gtk.gdk.pixbuf_new_from_data(
             buf, gtk.gdk.COLORSPACE_RGB,  True, 8, w, h, w*4)
-        pixmap.draw_pixbuf(pixmap.new_gc(), pixbuf, 0, 0, 0, 0, w, h,
+       g = pixmap.new_gc()
+        pixmap.draw_pixbuf(g, pixbuf, 0, 0, 0, 0, w, h,
                            gtk.gdk.RGB_DITHER_NONE, 0, 0)
+
+       print "XXXXXXXXXX", pixbuf,
g,pixbuf.__grefcount__,g.__grefcount__
+       print gc.get_referrers(pixbuf)
+       print gc.get_referrers(g)
+       del pixbuf
+       del g
+       gc.collect()
+
         if DEBUG: print 'FigureCanvasGTKAgg.render_figure done'

     def blit(self, bbox=None):


The __grefcount__ values are 1 but the memory is not freed up even after
gc.collect().

Mátyás János wrote:
> Hi,
> 
> I'm looking for memory leaks in a python application and found leaks in
> matplotlib. The application is graphic intensive. Each time it updates
> the screen, matplotlib allocates another 5-10 megabytes memory for the
> new gtk.gdk.Pixbuf and gtk.gdk.GCX11 while does not free up the buffers
> allocated for the previous content.
> 

This sounds to me like a pygtk bug, not a matplotlib bug; a gtk object 
is hanging around after its reference has been deleted. What versions of 
gtk and pygtk are you using?  This sounds dimly familiar.  I don't know 
enough about gtk and pygtk to help, but I am sure the people who do know 
more will want to know the version.

Eric

> I switched on garbage collection debugging with:
> 
> import gc
> gc.enable()
> gc.set_debug(gc.DEBUG_LEAK)
> 
> and tried to delete the leaking objects:
> 
> --- ./lib/matplotlib/backends/backend_gtkagg.py 2008-06-23
> 04:09:29.000000000 +0200 ++
> + /usr/lib/python2.4/site-packages/matplotlib-0.91.4-py2.4-linux-i686.egg/matplotlib/backends/backend_gtkagg.py
> 2008-10-02 00:05:32.000000000 +0200 @@ -3,6 +3,7 @@ """
>  from __future__ import division
>  import os
> +import gc
> 
>  import matplotlib
>  from matplotlib.figure import Figure
> @@ -82,8 +83,17 @@
>          h = int(ren.height)
>          pixbuf = gtk.gdk.pixbuf_new_from_data(
>              buf, gtk.gdk.COLORSPACE_RGB,  True, 8, w, h, w*4)
> -        pixmap.draw_pixbuf(pixmap.new_gc(), pixbuf, 0, 0, 0, 0, w, h,
> +       g = pixmap.new_gc()
> +        pixmap.draw_pixbuf(g, pixbuf, 0, 0, 0, 0, w, h,
>                             gtk.gdk.RGB_DITHER_NONE, 0, 0)
> +
> +       print "XXXXXXXXXX", pixbuf,
> g,pixbuf.__grefcount__,g.__grefcount__
> +       print gc.get_referrers(pixbuf)
> +       print gc.get_referrers(g)
> +       del pixbuf
> +       del g
> +       gc.collect()
> +
>          if DEBUG: print 'FigureCanvasGTKAgg.render_figure done'
> 
>      def blit(self, bbox=None):
> 
> 
> The __grefcount__ values are 1 but the memory is not freed up even after
> gc.collect().
> 
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Agreed.  I'm not sure how this bug could be resolved only on the 
matplotlib side.  See if you can make a standalone (pygtk-only) example 
that demonstrates this bug and send it to their mailing list.  Also, if 
it's possible, try updating pygtk.  There was a very similar bug in an 
earlier version (sorry, I can't find the reference), that was resolved.

Cheers,
Mike

Eric Firing wrote:
> Mátyás János wrote:
>   
>> Hi,
>>
>> I'm looking for memory leaks in a python application and found leaks in
>> matplotlib. The application is graphic intensive. Each time it updates
>> the screen, matplotlib allocates another 5-10 megabytes memory for the
>> new gtk.gdk.Pixbuf and gtk.gdk.GCX11 while does not free up the buffers
>> allocated for the previous content.
>>
>>     
>
> This sounds to me like a pygtk bug, not a matplotlib bug; a gtk object 
> is hanging around after its reference has been deleted. What versions of 
> gtk and pygtk are you using?  This sounds dimly familiar.  I don't know 
> enough about gtk and pygtk to help, but I am sure the people who do know 
> more will want to know the version.
>
> Eric
>
>   
>> I switched on garbage collection debugging with:
>>
>> import gc
>> gc.enable()
>> gc.set_debug(gc.DEBUG_LEAK)
>>
>> and tried to delete the leaking objects:
>>
>> --- ./lib/matplotlib/backends/backend_gtkagg.py 2008-06-23
>> 04:09:29.000000000 +0200 ++
>> + /usr/lib/python2.4/site-packages/matplotlib-0.91.4-py2.4-linux-i686.egg/matplotlib/backends/backend_gtkagg.py
>> 2008-10-02 00:05:32.000000000 +0200 @@ -3,6 +3,7 @@ """
>>  from __future__ import division
>>  import os
>> +import gc
>>
>>  import matplotlib
>>  from matplotlib.figure import Figure
>> @@ -82,8 +83,17 @@
>>          h = int(ren.height)
>>          pixbuf = gtk.gdk.pixbuf_new_from_data(
>>              buf, gtk.gdk.COLORSPACE_RGB,  True, 8, w, h, w*4)
>> -        pixmap.draw_pixbuf(pixmap.new_gc(), pixbuf, 0, 0, 0, 0, w, h,
>> +       g = pixmap.new_gc()
>> +        pixmap.draw_pixbuf(g, pixbuf, 0, 0, 0, 0, w, h,
>>                             gtk.gdk.RGB_DITHER_NONE, 0, 0)
>> +
>> +       print "XXXXXXXXXX", pixbuf,
>> g,pixbuf.__grefcount__,g.__grefcount__
>> +       print gc.get_referrers(pixbuf)
>> +       print gc.get_referrers(g)
>> +       del pixbuf
>> +       del g
>> +       gc.collect()
>> +
>>          if DEBUG: print 'FigureCanvasGTKAgg.render_figure done'
>>
>>      def blit(self, bbox=None):
>>
>>
>> The __grefcount__ values are 1 but the memory is not freed up even after
>> gc.collect().
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Matplotlib-devel mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>>     
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi,

thank you very much! The memory leak disappeared after I updated
pygobject from 2.12 to 2.13.2.