matplotlib-users

[Matplotlib-users] Segmentation fault under Agg

[Mike N. <mic...@sr...>]

I've encountered a segmentation fault using the Agg backend when making 
and saving a png plot.  The segmentation fault does not seem to occur 
under different backends (e.g. Cairo).

The sequence of commands amounts to making a plot, setting the limits of 
the plot, then saving the plot as a png using savefig.  If the value of 
one of the points is too large, a segmentation fault is generated.  
Obviously the simple work-around is to not plot the out-of-bounds 
points, but the segmentation fault is probably not the desired behavior! 

Below is an example, which generates a segmentation fault on matplotlib 
versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and 
CentOS 5.3).

Can others reproduce this issue?

Thanks,
Mike Nicolls


import scipy
import matplotlib
matplotlib.use('Agg')
import pylab

if __name__ == '__main__':
    
    xdata,ydata = scipy.rand(2,10)
    xdata[3]=1.0e9  # comment out to avoid seg fault
    
    pylab.figure()
    pylab.plot(xdata,ydata,'k.')
    pylab.xlim((0.0,1.0))
    
    pylab.savefig('test.png')

Re: [Matplotlib-users] Segmentation fault under Agg

[John H. <jd...@gm...>]

On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <mic...@sr...> wrote:
> I've encountered a segmentation fault using the Agg backend when making
> and saving a png plot.  The segmentation fault does not seem to occur
> under different backends (e.g. Cairo).
>
> The sequence of commands amounts to making a plot, setting the limits of
> the plot, then saving the plot as a png using savefig.  If the value of
> one of the points is too large, a segmentation fault is generated.
> Obviously the simple work-around is to not plot the out-of-bounds
> points, but the segmentation fault is probably not the desired behavior!
>
> Below is an example, which generates a segmentation fault on matplotlib
> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
> CentOS 5.3).
>
> Can others reproduce this issue?

Thanks for the report -- I can confirm this on OSX and linux on svn HEAD

I've made minor tweaks to your test case to make it deterministic::

    import numpy as np
    import matplotlib
    matplotlib.use('Agg')
    import matplotlib.pyplot as plt

    xdata = np.arange(10.0)
    ydata = np.arange(10.0)

    xdata[3]=1.0e9  # comment out to avoid seg fault

    fig = plt.figure()
    ax = fig.add_subplot(111)
    ax.plot(xdata,ydata,'k.')
    ax.set_xlim(0.0,1.0)

    fig.savefig('test.png')


and added a bug report to :

  https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720

Platforms confirmed w/ bug:

home:~> uname -a
Darwin Macintosh-8.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

jdhunter@uqbar:~> uname -a
Linux uqbar 2.6.27-14-generic #1 SMP Tue Jun 30 19:54:46 UTC 2009
x86_64 GNU/Linux

Re: [Matplotlib-users] Segmentation fault under Agg

[John H. <jd...@gm...>]

On Wed, Sep 23, 2009 at 10:15 PM, John Hunter <jd...@gm...> wrote:
> On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <mic...@sr...> wrote:
>> I've encountered a segmentation fault using the Agg backend when making
>> and saving a png plot.  The segmentation fault does not seem to occur
>> under different backends (e.g. Cairo).
>>
>> The sequence of commands amounts to making a plot, setting the limits of
>> the plot, then saving the plot as a png using savefig.  If the value of
>> one of the points is too large, a segmentation fault is generated.
>> Obviously the simple work-around is to not plot the out-of-bounds
>> points, but the segmentation fault is probably not the desired behavior!
>>
>> Below is an example, which generates a segmentation fault on matplotlib
>> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
>> CentOS 5.3).
>>
>> Can others reproduce this issue?
>
> Thanks for the report -- I can confirm this on OSX and linux on svn HEAD
>
> I've made minor tweaks to your test case to make it deterministic::

I applied the following patch to the branch and head -- it feels like there
would be a more elegant way to handle it, so I'd like Michael at least to
take a look at it::

home:~/mpl> svn diff -rPREV:HEAD src/_backend_agg.cpp
Index: src/_backend_agg.cpp
===================================================================
--- src/_backend_agg.cpp (revision 7820)
+++ src/_backend_agg.cpp (revision 7821)
@@ -608,6 +608,14 @@

x = (double)(int)x; y = (double)(int)y;

+ // if x or y is close to the width or height, the filled
+ // region could be inside the boundary even if the center is
+ // out. But at some point we need to cull these points
+ // because they can create segfaults of they overflow; eg
+ //
https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
+ if (fabs(x)>(2*width)) continue;
+ if (fabs(y)>(2*height)) continue;
+
pixfmt_amask_type pfa(pixFmt, alphaMask);
amask_ren_type r(pfa);
amask_aa_renderer_type ren(r);
@@ -629,6 +637,14 @@

x = (double)(int)x; y = (double)(int)y;

+ // if x or y is close to the width or height, the filled
+ // region could be inside the boundary even if the center is
+ // out. But at some point we need to cull these points
+ // because they can create segfaults of they overflow; eg
+ //
https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
+ if (fabs(x)>(2*width)) continue;
+ if (fabs(y)>(2*height)) continue;
+
if (face.first) {
rendererAA.color(face.second);
sa.init(fillCache, fillSize, x, y);

Re: [Matplotlib-users] Segmentation fault under Agg

[Michael D. <md...@st...>]

I committed a slightly tighter version of this that uses a rectangle 
based on the size of the image plus a border to accomodate the exact 
marker size.  Probably makes very little difference, but I suppose if 
there was a dense field of markers outside of view, this might speed 
things up a bit more.

A further optimization might be to use the clipping rectangle, but 
that's not necessary merely to prevent the segfault.

Mike

On 09/24/2009 12:06 AM, John Hunter wrote:
> On Wed, Sep 23, 2009 at 10:15 PM, John Hunter<jd...@gm...>  wrote:
>    
>> On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls<mic...@sr...>  wrote:
>>      
>>> I've encountered a segmentation fault using the Agg backend when making
>>> and saving a png plot.  The segmentation fault does not seem to occur
>>> under different backends (e.g. Cairo).
>>>
>>> The sequence of commands amounts to making a plot, setting the limits of
>>> the plot, then saving the plot as a png using savefig.  If the value of
>>> one of the points is too large, a segmentation fault is generated.
>>> Obviously the simple work-around is to not plot the out-of-bounds
>>> points, but the segmentation fault is probably not the desired behavior!
>>>
>>> Below is an example, which generates a segmentation fault on matplotlib
>>> versions 0.99.0 (run on OS X 10.5.8) and 0.98.5.2 (run on Fedora 11 and
>>> CentOS 5.3).
>>>
>>> Can others reproduce this issue?
>>>        
>> Thanks for the report -- I can confirm this on OSX and linux on svn HEAD
>>
>> I've made minor tweaks to your test case to make it deterministic::
>>      
> I applied the following patch to the branch and head -- it feels like there
> would be a more elegant way to handle it, so I'd like Michael at least to
> take a look at it::
>
> home:~/mpl>  svn diff -rPREV:HEAD src/_backend_agg.cpp
> Index: src/_backend_agg.cpp
> ===================================================================
> --- src/_backend_agg.cpp (revision 7820)
> +++ src/_backend_agg.cpp (revision 7821)
> @@ -608,6 +608,14 @@
>
> x = (double)(int)x; y = (double)(int)y;
>
> + // if x or y is close to the width or height, the filled
> + // region could be inside the boundary even if the center is
> + // out. But at some point we need to cull these points
> + // because they can create segfaults of they overflow; eg
> + //
> https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
> + if (fabs(x)>(2*width)) continue;
> + if (fabs(y)>(2*height)) continue;
> +
> pixfmt_amask_type pfa(pixFmt, alphaMask);
> amask_ren_type r(pfa);
> amask_aa_renderer_type ren(r);
> @@ -629,6 +637,14 @@
>
> x = (double)(int)x; y = (double)(int)y;
>
> + // if x or y is close to the width or height, the filled
> + // region could be inside the boundary even if the center is
> + // out. But at some point we need to cull these points
> + // because they can create segfaults of they overflow; eg
> + //
> https://sourceforge.net/tracker/?func=detail&aid=2865490&group_id=80706&atid=560720
> + if (fabs(x)>(2*width)) continue;
> + if (fabs(y)>(2*height)) continue;
> +
> if (face.first) {
> rendererAA.color(face.second);
> sa.init(fillCache, fillSize, x, y);
>
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