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From: Wayne E. H. <wh...@pa...> - 2007-10-02 05:59:07
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I have a serious problem with my Linux installation of matplotlib. It segfaults after a very brief display of a plot window outline (no actual plot within it). Before presenting the details of my problem, I would like to download the latest CVS version to make sure this hasn't been fixed already, however I cannot find any references to CVS in any of the Matplotlib web pages, except for a reference for it in one of the recent emails in this list. How do I find it ? Thanks in advance, Wayne |
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From: <jk...@ik...> - 2007-10-02 06:49:13
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"Wayne E. Harlan" <wh...@pa...> writes: > I cannot find any references to CVS in any of the Matplotlib web pages The code is in a Subversion repository: http://sourceforge.net/svn/?group_id=80706 (You probably want to add "/trunk" to the URL as mentioned in the "warning" paragraph.) > It segfaults after a very brief display of a plot window outline (no > actual plot within it). There are some instructions for debugging segfaults in the SEGFAULTS file. -- Jouni K. Seppänen http://www.iki.fi/jks |
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From: Eric F. <ef...@ha...> - 2007-10-02 07:32:58
|
Wayne E. Harlan wrote: > I have a serious problem with my Linux installation of matplotlib. It > segfaults after a very brief display of a plot window outline (no actual > plot within it). Before presenting the details of my problem, I would If a straightforward plotting sequence, such as one of the examples, does this, then it sounds like a broken installation, not a matplotlib bug. > like to download the latest CVS version to make sure this hasn't been > fixed already, however I cannot find any references to CVS in any of the > Matplotlib web pages, except for a reference for it in one of the recent > emails in this list. How do I find it ? See the following: http://sourceforge.net/svn/?group_id=80706 We are using subversion, not cvs. Eric > > Thanks in advance, > > Wayne |
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From: Wayne E. H. <wh...@pa...> - 2007-10-03 02:55:14
Attachments:
simple_output
strace_output
|
Eric Firing wrote:
> If a straightforward plotting sequence, such as one of the examples,
> does this, then it sounds like a broken installation, not a matplotlib
> bug.
>
Based on your comment above, here are my particulars:
1) System is LinuxFromScratch recently built from their SVN book:
glibc is 2.5, gcc is 4.1.2, X is Xorg 7.2 installed in /usr.
2) Python 2.5.1 with Tkinter enabled. If I run the following script,
I get the 'quit' button which when clicked makes the button/window
disappear, so I know python and Tkinter are working.
#!/usr/bin/python
from Tkinter import *
class Application(Frame):
def __init__(self, master=None):
Frame.__init__(self, master)
self.grid()
self.createWidgets()
def createWidgets(self):
self.quitButton = Button ( self, text="Quit",command=self.quit )
self.quitButton.grid()
app = Application()
app.master.title("Sample application")
app.mainloop()
3) Numpy 1.0.3.1 installed without any errors and I can do the following:
>>> import numpy
>>> List = dir(numpy)
>>> len(List)
491
>>>
4) Matplotlib 0.90.1 also installed without error. I set
BUILD_TKAGG = 1 which may not have been necessary, but it seems to
have worked since in my matplotlibrc file I find "backend :
TkAgg". Then if I do this
" python simple_plot.py --verbose-debug", I get the output in the
simple_output attachment. The font errors there are the same as what I
get in each of my 3 XP installations where matplotlib works just fine,
so I don't think they are the cause of the segfault. As I may have
described previously, the plot window appears for a fraction of a second
and then disappears as the segfault occurs.
I also ran "strace python simple_plot.py --verbose-debug" with the
output that's in the strace_output attachment to see if that would give
any more information but that output ends at the segfault and I am not
knowledgeable enough to understand what it says.
Any help will be appreciated.
Best Regards,
Wayne
|
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From: Michael D. <md...@st...> - 2007-10-03 19:02:21
|
I'll second Eric's suggestion.
It might also help to have a backtrace from gdb in addition to your
strace output.
Cheers,
Mike
Wayne E. Harlan wrote:
> Eric Firing wrote:
>> If a straightforward plotting sequence, such as one of the examples,
>> does this, then it sounds like a broken installation, not a matplotlib
>> bug.
>>
> Based on your comment above, here are my particulars:
>
> 1) System is LinuxFromScratch recently built from their SVN book:
> glibc is 2.5, gcc is 4.1.2, X is Xorg 7.2 installed in /usr.
>
> 2) Python 2.5.1 with Tkinter enabled. If I run the following script,
> I get the 'quit' button which when clicked makes the button/window
> disappear, so I know python and Tkinter are working.
>
> #!/usr/bin/python
> from Tkinter import *
> class Application(Frame):
> def __init__(self, master=None):
> Frame.__init__(self, master)
> self.grid()
> self.createWidgets()
> def createWidgets(self):
> self.quitButton = Button ( self, text="Quit",command=self.quit )
> self.quitButton.grid()
> app = Application()
> app.master.title("Sample application")
> app.mainloop()
>
> 3) Numpy 1.0.3.1 installed without any errors and I can do the following:
>
> >>> import numpy
> >>> List = dir(numpy)
> >>> len(List)
> 491
> >>>
>
> 4) Matplotlib 0.90.1 also installed without error. I set
> BUILD_TKAGG = 1 which may not have been necessary, but it seems to
> have worked since in my matplotlibrc file I find "backend :
> TkAgg". Then if I do this
> " python simple_plot.py --verbose-debug", I get the output in the
> simple_output attachment. The font errors there are the same as what I
> get in each of my 3 XP installations where matplotlib works just fine,
> so I don't think they are the cause of the segfault. As I may have
> described previously, the plot window appears for a fraction of a second
> and then disappears as the segfault occurs.
>
> I also ran "strace python simple_plot.py --verbose-debug" with the
> output that's in the strace_output attachment to see if that would give
> any more information but that output ends at the segfault and I am not
> knowledgeable enough to understand what it says.
>
> Any help will be appreciated.
>
> Best Regards,
>
> Wayne
>
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
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|
|
From: Eric F. <ef...@ha...> - 2007-10-03 18:56:12
|
Wayne,
I'm stumped. Do you get a segfault only with the gui backend? Can you
you do this:
import matplotlib
matplotlib.use('Agg')
import pylab
pylab.plot([1,2,3])
pylab.savefig('test.png')
Eric
Wayne E. Harlan wrote:
> Eric Firing wrote:
>> If a straightforward plotting sequence, such as one of the examples,
>> does this, then it sounds like a broken installation, not a matplotlib
>> bug.
>>
> Based on your comment above, here are my particulars:
>
> 1) System is LinuxFromScratch recently built from their SVN book:
> glibc is 2.5, gcc is 4.1.2, X is Xorg 7.2 installed in /usr.
>
> 2) Python 2.5.1 with Tkinter enabled. If I run the following script,
> I get the 'quit' button which when clicked makes the button/window
> disappear, so I know python and Tkinter are working.
>
> #!/usr/bin/python
> from Tkinter import *
> class Application(Frame):
> def __init__(self, master=None):
> Frame.__init__(self, master)
> self.grid()
> self.createWidgets()
> def createWidgets(self):
> self.quitButton = Button ( self, text="Quit",command=self.quit )
> self.quitButton.grid()
> app = Application()
> app.master.title("Sample application")
> app.mainloop()
>
> 3) Numpy 1.0.3.1 installed without any errors and I can do the following:
>
> >>> import numpy
> >>> List = dir(numpy)
> >>> len(List)
> 491
> >>>
>
> 4) Matplotlib 0.90.1 also installed without error. I set
> BUILD_TKAGG = 1 which may not have been necessary, but it seems to
> have worked since in my matplotlibrc file I find "backend :
> TkAgg". Then if I do this
> " python simple_plot.py --verbose-debug", I get the output in the
> simple_output attachment. The font errors there are the same as what I
> get in each of my 3 XP installations where matplotlib works just fine,
> so I don't think they are the cause of the segfault. As I may have
> described previously, the plot window appears for a fraction of a second
> and then disappears as the segfault occurs.
>
> I also ran "strace python simple_plot.py --verbose-debug" with the
> output that's in the strace_output attachment to see if that would give
> any more information but that output ends at the segfault and I am not
> knowledgeable enough to understand what it says.
>
> Any help will be appreciated.
>
> Best Regards,
>
> Wayne
>
>
> ------------------------------------------------------------------------
>
> [wayne@holmes] ~/Programming/Python/matplotlib/examples: python simple_plot.py --verbose-debug
> matplotlib data path /usr/lib/python2.5/site-packages/matplotlib/mpl-data
> $HOME=/home/wayne
> CONFIGDIR=/home/wayne/.matplotlib
> loaded rc file /home/wayne/.matplotlib/matplotlibrc
> matplotlib version 0.90.1
> verbose.level debug
> interactive is False
> units is True
> platform is linux2
> loaded modules: ['pylab', 'distutils.distutils', '_bisect', '__future__', 'copy_reg',
> 'sre_compile', 'distutils', 'itertools', '_hashlib', '_sre', '__main__', 'site', '__
> builtin__', 'datetime', 'matplotlib.re', 'matplotlib.tempfile', 'encodings', 'encodin
> gs.encodings', 'shutil', 'distutils.string', 'dateutil', 'matplotlib.datetime', 'posi
> xpath', '_random', 'tempfile', 'errno', 'matplotlib.warnings', 'binascii', 'encodings
> .codecs', 'sre_constants', 're', 'matplotlib.md5', 'os.path', 'pytz.sys', '_codecs',
> 'distutils.sysconfig', 'pytz.sets', 'math', 'fcntl', 'stat', 'zipimport', 'string', '
> warnings', 'encodings.types', 'UserDict', 'encodings.ascii', 'matplotlib.sys', 'matpl
> otlib', 'distutils.os', 'sys', 'pytz.tzinfo', 'pytz', 'pytz.datetime', 'matplotlib.__
> future__', 'codecs', 'distutils.re', 'matplotlib.pytz', 'types', 'md5', '_types', 'ma
> tplotlib.dateutil', 'hashlib', 'matplotlib.os', 'thread', 'bisect', 'matplotlib.distu
> tils', 'signal', 'distutils.errors', 'random', 'linecache', 'matplotlib.shutil', 'pos
> ix', 'encodings.aliases', 'sets', 'exceptions', 'sre_parse', 'pytz.bisect', 'distutil
> s.sys', 'os', 'strop']
> numerix numpy 1.0.3.1
> font search path ['/usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf', '
> /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/afm']
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/VeraMo
> BI.ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/VeraSe
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/VeraSe
> Bd.ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmsy10
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/VeraIt
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.
> ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10
> .ttf
> trying fontname /usr/lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.t
> tf
> loaded ttfcache file /home/wayne/.matplotlib/ttffont.cache
> backend TkAgg version 8.4
> findfont failed Bitstream Vera Serif, New Century Schoolbook, Century Schoolb
> ook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Pala
> tino, Charter, serif
> Could not match Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, U
> topia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Ch
> arter, serif, normal, normal. Returning /usr/lib/python2.5/site-packages/matplotlib/
> mpl-data/fonts/ttf/Vera.ttf
> findfont failed Bitstream Vera Serif, New Century Schoolbook, Century Schoolb
> ook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Pala
> tino, Charter, serif, normal, normal 400, normal, 14.0
> Could not match Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, U
> topia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Ch
> arter, serif, normal, normal. Returning /usr/lib/python2.5/site-packages/matplotlib/
> mpl-data/fonts/ttf/Vera.ttf
> Segmentation fault (core dumped)
> [wayne@holmes] ~/Programming/Python/matplotlib/examples:
>
>
> ------------------------------------------------------------------------
>
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> munmap(0xb6301000, 1921024) = 0
> munmap(0xb64d6000, 1921024) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> lstat64("/usr", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> lstat64("/usr/lib", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
> lstat64("/usr/lib/tk8.4", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> open("/usr/lib/tk8.4/tclIndex", O_RDONLY|O_LARGEFILE) = 6
> fcntl64(6, F_SETFD, FD_CLOEXEC) = 0
> ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0xbfcdda28) = -1 ENOTTY (Inappropriate ioctl for device)
> read(6, "# Tcl autoload index file, versi"..., 4096) = 4096
> read(6, "]]\nset auto_index(::tk::FocusGro"..., 4096) = 4096
> read(6, "::tk::MenuDownArrow) [list sourc"..., 4096) = 4096
> read(6, " [list source [file join $dir sp"..., 4096) = 4096
> read(6, "\nset auto_index(::tk::IconList_A"..., 4096) = 4096
> read(6, "_InterpFilter) [list source [fil"..., 4096) = 1730
> read(6, "", 4096) = 0
> close(6) = 0
> lstat64("/usr", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> lstat64("/usr/lib", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
> open("/usr/lib/tclIndex", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory)
> lstat64("/usr", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> lstat64("/usr/lib", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
> lstat64("/usr/lib/tcl8.4", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> open("/usr/lib/tcl8.4/tclIndex", O_RDONLY|O_LARGEFILE) = 6
> fcntl64(6, F_SETFD, FD_CLOEXEC) = 0
> ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0xbfcdda28) = -1 ENOTTY (Inappropriate ioctl for device)
> read(6, "# Tcl autoload index file, versi"..., 4096) = 4096
> read(6, "Name) [list source [file join $d"..., 4096) = 2001
> read(6, "", 4096) = 0
> close(6) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> futex(0x81d3cc0, FUTEX_WAKE, 1) = 0
> --- SIGSEGV (Segmentation fault) @ 0 (0) ---
> +++ killed by SIGSEGV (core dumped) +++
> Process 1826 detached
> [wayne@holmes] ~/Programming/Python/matplotlib/examples:
|
|
From: Wayne E. H. <wh...@pa...> - 2007-10-04 02:26:25
Attachments:
test.png
|
Eric Firing wrote:
> Wayne,
>
> I'm stumped. Do you get a segfault only with the gui backend? Can
> you you do this:
>
> import matplotlib
> matplotlib.use('Agg')
> import pylab
> pylab.plot([1,2,3])
> pylab.savefig('test.png')
>
> Eric
<previous stuff snipped>
OK, this worked. I have attached the test,png file that resulted. But
I don't quite know what this means ...
IDLE 1.2.1
>>> import matplotlib
>>> matplotlib.use('Agg')
>>> import pylab
>>> pylab.plot([1,2,3])
[<matplotlib.lines.Line2D instance at 0x87cd56c>]
>>> pylab.savefig('test.png')
>>>
The other suggestion from Michael about using gdb will have to wait
until I download, install and learn to use it, but if that's required,
that's what I'll do.
Thanks
Wayne
|
|
From: Eric F. <ef...@ha...> - 2007-10-04 02:53:36
|
Wayne,
Segfaults are generally caused by problems in extension code or
libraries. The fact that the plotting works with a non-gui backend
indicates that the problem is not in matplotlib's transform or Agg
extension code, or in the bits of numpy code that get used along the
way. I was pretty sure this would be the case; all of those components
are solid and well-tested together, at least for simple plotting.
That tends to throw suspicion on Tkinter/Tk/Tcl or one of mpl's
extension bits that is run with Tk. I'm not sure there are any in this
case.
One way to narrow it down is to try another gui: gtk or qt. Do you have
either of these libraries installed?
Eric
Wayne E. Harlan wrote:
>
>
> Eric Firing wrote:
>> Wayne,
>>
>> I'm stumped. Do you get a segfault only with the gui backend? Can
>> you you do this:
>>
>> import matplotlib
>> matplotlib.use('Agg')
>> import pylab
>> pylab.plot([1,2,3])
>> pylab.savefig('test.png')
>>
>> Eric
> <previous stuff snipped>
>
> OK, this worked. I have attached the test,png file that resulted. But
> I don't quite know what this means ...
>
> IDLE 1.2.1 >>> import matplotlib
> >>> matplotlib.use('Agg')
> >>> import pylab
> >>> pylab.plot([1,2,3])
> [<matplotlib.lines.Line2D instance at 0x87cd56c>]
> >>> pylab.savefig('test.png')
> >>>
>
> The other suggestion from Michael about using gdb will have to wait
> until I download, install and learn to use it, but if that's required,
> that's what I'll do.
>
> Thanks
>
> Wayne
>
>
> ------------------------------------------------------------------------
>
|
|
From: Wayne E. H. <wh...@pa...> - 2007-10-04 05:50:52
|
Eric:
First thanks for all the help. Here's the scoop after I replied to your
earlier post. I thought a bit about the sense of where you were going
(it always helps to think a bit). So I decided to try compiling
matplotlib with the GTK backend instead of Tk. I have gtk-2.11.5. So
I did some sed's to the setup.py file:
sed -i "s|BUILD_GTKAGG = 'auto'|BUILD_GTKAGG = 1|" setup.py &&
sed -i "s|BUILD_GTK = 'auto'|BUILD_GTK = 1|" setup.py &&
sed -i "s|BUILD_TKAGG = 'auto'|BUILD_TKAGG = 0|" setup.py &&
and then proceeded. It turned out that I needed pygtk, so I downloaded
that and installed it, but pygtk still complained about not having
pycairo (which it says is optional), so I downloaded that. Making a
long story short, installing pycairo-1.4.0, pyobject-2.14.0,
pygtk-2.10.6 and then reinstalling matplotlib with the above sed's did
the trick. I'm displaying all the plots I have been able to in XP (so I
don't need XP any more, at least at home).
Once again, thanks for the suggestions. Although I'm set here, I wonder
about the tcl/tk issue with matplotlib. I am using tcl/tk-8.4.15. I
wonder if it's too new ? Or is there some other package that is needed ?
Wayne
Eric Firing wrote:
> Wayne,
>
> Segfaults are generally caused by problems in extension code or
> libraries. The fact that the plotting works with a non-gui backend
> indicates that the problem is not in matplotlib's transform or Agg
> extension code, or in the bits of numpy code that get used along the
> way. I was pretty sure this would be the case; all of those
> components are solid and well-tested together, at least for simple
> plotting.
>
> That tends to throw suspicion on Tkinter/Tk/Tcl or one of mpl's
> extension bits that is run with Tk. I'm not sure there are any in
> this case.
>
> One way to narrow it down is to try another gui: gtk or qt. Do you
> have either of these libraries installed?
>
> Eric
>
> Wayne E. Harlan wrote:
>>
>>
>> Eric Firing wrote:
>>> Wayne,
>>>
>>> I'm stumped. Do you get a segfault only with the gui backend? Can
>>> you you do this:
>>>
>>> import matplotlib
>>> matplotlib.use('Agg')
>>> import pylab
>>> pylab.plot([1,2,3])
>>> pylab.savefig('test.png')
>>>
>>> Eric
>> <previous stuff snipped>
>>
>> OK, this worked. I have attached the test,png file that resulted.
>> But I don't quite know what this means ...
>>
>> IDLE 1.2.1 >>> import matplotlib
>> >>> matplotlib.use('Agg')
>> >>> import pylab
>> >>> pylab.plot([1,2,3])
>> [<matplotlib.lines.Line2D instance at 0x87cd56c>]
>> >>> pylab.savefig('test.png')
>> >>>
>>
>> The other suggestion from Michael about using gdb will have to wait
>> until I download, install and learn to use it, but if that's
>> required, that's what I'll do.
>>
>> Thanks
>>
>> Wayne
>>
>>
>> ------------------------------------------------------------------------
>>
>
>
|
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