Segmentation fault under Agg

Community matplotlib-users
#1

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')

#2

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@...2795...:~> uname -a
Linux uqbar 2.6.27-14-generic #1 SMP Tue Jun 30 19:54:46 UTC 2009
x86_64 GNU/Linux

···

On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <michael.nicolls@...392...> 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?

#3

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

···

On Wed, Sep 23, 2009 at 10:15 PM, John Hunter <jdh2358@...287...> wrote:

On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls <michael.nicolls@...392...> 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::

===================================================================
--- 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);

#4

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<jdh2358@...287...> wrote:
   

On Wed, Sep 23, 2009 at 6:47 PM, Mike Nicolls<michael.nicolls@...392...> 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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