Re: [Matplotlib-users] segfaults in ipython

[Steve S. <el...@gm...>]

John Hunter wrote:
>>>>>>"Steve" == Steve Schmerler <el...@gm...> writes:
> 
> 
>     Steve> Hi I recently posted something about segfaults I get when
>     Steve> plotting. Now here is a little update and I really hope
>     Steve> someone has an idea how I can solve this problem.
> 
>     Steve> I'm running IPython 0.6.13 on a Debian box, installed the
>     Steve> recent mpl 0.83.2 from source, GTKAgg backend.
> 
>     Steve> 1)
> 
>     Steve> When I start ipython (as normal user) with the -pylab
>     Steve> option and then say
> 
>     Steve> 	plot([1,2,3])
> 
>     Steve> I get
> 
>     Steve> In [1]: plot([1,2,3])
>     Steve> ---------------------------------------------------------------------------
>     Steve> exceptions.SystemError Traceback (most recent call last)
> 
> 
>     Steve> SystemError: ../Objects/moduleobject.c:48: bad argument to
>     Steve> internal function
> 
> You say this is a segfault, but it looks like an exception.  Does this
> actually kill the ipython shell?  Is this a full posting of the
> traceback?

I upgraded to IPython 0.6.15 (installed from source), the former 0.6.13 
was apt-get installed on Debian (sarge, stable).

Actually, it is a segfault, and it kills the IPython shell.

###############################################################################

elcorto@bach:~/Install/IPython$ ipython -pylab
/usr/lib/python2.3/site-packages/IPython/Shell.py:627: 
GtkDeprecationWarning: gtk.timeout_add is deprecated, use 
gobject.timeout_add instead
   self.gtk.timeout_add(self.TIMEOUT, self.on_timer)
Python 2.3.5 (#2, May  4 2005, 08:51:39)
Type "copyright", "credits" or "license" for more information.

IPython 0.6.15 -- An enhanced Interactive Python.
?       -> Introduction to IPython's features.
%magic  -> Information about IPython's 'magic' % functions.
help    -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.

   Welcome to pylab, a matplotlib-based Python environment.
   For more information, type 'help(pylab)'.

In [1]: plot([1,2,3])
---------------------------------------------------------------------------
exceptions.SystemError                               Traceback (most 
recent call last)


SystemError: ../Objects/moduleobject.c:48: bad argument to internal function
Speicherzugriffsfehler
elcorto@bach:~/Install/IPython$

#################################################################################

At least "Speicherzugriffsfehler" is german for segfault :)

I still can plot as root, but not as user!? If it's some kind of 
permission problem it would be good to know something about
"../Objects/moduleobject.c". I there a way to get IPython to print the 
full path?

BTW, Fernando mentioned earlier that this GtkDeprecationWarning would go 
away if I upgrade to IPython 0.6.15 but unfortunately it's still there.

> 
> What happens if you run the following script outside of ipython
> 
>     from pylab import plot, show
>     plot([1,2,3])
>     show()
> 
> with 
> 
>   > python test.py --verbose-helpful 
> 
> Does this create a proper figure window -- please post all output from
> the script.
> 

This works, a window shows up.

#################################################################################

elcorto@bach:~/Install/IPython$ python test.py --verbose-helpful
matplotlib data path /usr/share/matplotlib
$HOME=/home/elcorto
CONFIGDIR=/home/elcorto/.matplotlib
loaded rc file /usr/share/matplotlib/matplotlibrc
matplotlib version 0.83.2
verbose.level helpful
interactive is False
platform is linux2
numerix Numeric 23.8
font search path ['/usr/share/matplotlib']
loaded ttfcache file /home/elcorto/.matplotlib/ttffont.cache
backend GTKAgg version 2.6.1

#################################################################################

> 
>     Steve> 2)
> 
>     Steve> However when I change to root
> 
>     Steve> 	su <pwd>
> 
>     Steve> 	ipython -pylab
> 
>     Steve> then plotting works fine!?
> 
> Perhaps this has something to do with having permission to connect to
> the X11 server?  As a normal user, can you launch graphical apps from
> the shell, eg 
> 
>  > gedit&
> 

I can do that.

> 
> Have you done anything unusual with your system, changed the default
> permission bits, done a chroot, etc?  What linux distro are you
> running?
> 
> 
>     Steve> I have no idea where this moduleobject.c lives or to which
>     Steve> application it belongs.
> 
>     Steve> 2)
> 
>     Steve> If I try the same with the normal python interpreter
> 
>     Steve> 	python
> 
>     Steve> 	from pylab import *; ion() plot([1,2,3])
> 
>     Steve> a plot window pops up but shows no picture (no matter if
>     Steve> I'm root or not).
> 
> 

Debian sarge, stable. I'm not a Linux expert but it's a pretty fresh 
installation (on my computer at work) and I can't see what I should have 
done wrong. In fact I installed mpl on my (the same) Debian at home and 
it works fine there (OK it's mpl 0.81 and IPython 0.6.13).

> GTKAgg is not expected to work unless you are in a special threaded
> environment like ipython with -gthread or -pylab.  Try the same with
> the TkAgg backend (edit your rc file) and let me know what happens.
> 

Uh, I didn't build TkAgg, So I set BUILD_TKAGG = 'auto', but

	python setup.py build

fails:

[...]

src/_tkagg.cpp:26:19: tk.h: Datei oder Verzeichnis nicht gefunden (file
not found)

[...]

error: command 'gcc' failed with exit status 1

Do I have to install something besides python-tk?

> The last thing I'd advise is upgrading your ipython to the latest.
> 
> I've never seen this one before so I'm flying by the seat of my pants.
> 
> 

I hope we can sort this out.

cheers,
steve