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bbolker opened this issue Mar 11, 2015 · 13 comments
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segfault: fill_between with Python3 #4210

bbolker opened this issue Mar 11, 2015 · 13 comments
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backend: agg
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v2.0.0

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@bbolker
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bbolker commented Mar 11, 2015

I'm getting a reproducible segfault using fill_between in Python 3, but not Python 2, on Ubuntu 12.04 but not on MacOS (these are slightly different versions of Python3/matplotlib, and the Ubuntu is sitting in a virtual box/on a virtual filesystem).

I can try to update my Python3 version, but I'm curious whether anyone else has seen this.

Linux: ubuntu-10-new 3.2.0-77-generic-pae #112-Ubuntu, Python3 version 3.2.3 (matplotlib 1.5.dev1), Python 2.7.3 (matplotlib 1.1.1rc)
MacOS: 10.9.5 (13.4.0 Darwin Kernel Version 13.4.0), Python3 3.4.2 (matplotlib 1.4.2), Python 2.7.3 (matplotlib 1.1.1)

import numpy as np
from matplotlib import pyplot as plt

def u(t,shift=0):
    b = np.logical_and(shift<t,t<(1+shift))
    return(b.astype(float))

t = np.arange(0,2,1/40.)
plt.plot(t,u(t),color="red")
plt.ylim(0,1.25)
plt.xlim(-1,3)
plt.fill_between(t,u(t),facecolor="red",alpha=0.5)
plt.plot(t,u(t,0.75),color="blue")
plt.fill_between(t,u(t,0.75),facecolor="blue",alpha=0.5)

plt.savefig("fill_between.png")
@jenshnielsen
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Which version of matplotlib? I cannot reproduce it with Matplotlib 1.4.3 on Conda (Python 3.4.3) on Ubuntu 14.04

@bbolker
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bbolker commented Mar 11, 2015

1.5.dev1 (I edited my report above to include all the matplotlib versions) [I'm not sure how I ended up with development version!]

@mdboom mdboom self-assigned this Mar 11, 2015
@mdboom
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mdboom commented Mar 11, 2015

I'm having trouble reproducing this. Do you know the githash of the development version of matplotlib you are running? (1.5.dev1 doesn't uniquely identify a version, but just means it's "current git master"). I think it's possible this bug has already been fixed.

@bbolker
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bbolker commented Mar 11, 2015

still getting segfault with latest version installed (after a bit of struggle). This is on a 32-bit (virtual) system, I wonder if there's a possibility that that's the issue?

@mdboom mdboom removed their assignment Mar 11, 2015
@mdboom
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mdboom commented Mar 11, 2015

Ah -- I didn't try on a 32-bit system. Let's see if that helps me reproduce.

@mdboom
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mdboom commented Mar 11, 2015

I tried to replicate your environment as best I could -- Debian 32-bit, Python 3.2.3, matplotlib master. Still can't reproduce. What version of Numpy is involved here?

@bbolker
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bbolker commented Mar 11, 2015

1.9.1 . Sorry this is such a hassle. I can live without it as long as it's not causing anyone else any trouble ...

@tacaswell tacaswell added this to the Color overhaul milestone Mar 11, 2015
@mdboom
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mdboom commented Mar 11, 2015

Hmm... I was using the same Numpy. So I guess it remains a mystery.

If you're able to get a traceback from gdb for the segfault that might help.

Short instructions:

gdb `which python3`
run /path/to/example_script
bt

@bbolker
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bbolker commented Mar 11, 2015

gdb output:

Starting program: /usr/bin/python3 ~/classes/math1mp3/math1mp/notes/fill_between.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/i386-linux-gnu/libthread_db.so.1".
[New Thread 0xb6579b40 (LWP 11674)]

Program received signal SIGSEGV, Segmentation fault.
agg::rasterizer_cells_aa<agg::cell_aa>::line (this=0xa3f550c, x1=715827882, 
    y1=-90721, x2=713031679, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:320
320     void rasterizer_cells_aa<Cell>::line(int x1, int y1, int x2, int y2)

Beginning of backtrace:

#0  agg::rasterizer_cells_aa<agg::cell_aa>::line (this=0xa3f550c, 
    x1=715827882, y1=-90721, x2=713031679, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:320
#1  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=710235476, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#2  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=704643071, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#3  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=693458260, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#4  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=671088639, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#5  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=626349396, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#6  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (
    this=0xa3f550c, x1=715827882, y1=-90721, x2=536870911, y2=-90721)
    at extern/agg24-svn/include/agg_rasterizer_cells_aa.h:330
#7  0xb5d37c5e in agg::rasterizer_cells_aa<agg::cell_aa>::line (

... seems to go on nearly identically for a long time after this.

I'm happy to continue with this if it's helpful or drop it if it's not.

@tacaswell
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8000

Can you try deleting everything about your mpl install and the re-installing from current master? I am a bit worried that what is happening is that you have a mixture of old and new c++ extensions (as you commented you were unsure on how the dev version got installed) that are stepping on each other's toes.

@bbolker
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bbolker commented Mar 12, 2015

I will try; I may not have time for a couple of days (thanks for your patience).

@tacaswell tacaswell modified the milestones: Color overhaul, next major release (2.0) Oct 26, 2015
@QuLogic
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QuLogic commented Jan 7, 2016

Ping?

@tacaswell
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Closing due to inactivity and this not failing on travis.

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