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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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 Posted: Sat Aug 25, 2012 2:30 pm Post subject: [SOLVED] backtrace a segmentation fault using gdb |
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I'm trying to run a python script on my gentoo machine which I wrote on a different computer running linux mint. It uses numpy, wxpython and matplotlib and runs just fine on the linux mint machine. However when I try to run it on the gentoo machine I get a segmentation fault. The interesting thing is that the program seems to run until the end, since the last line in the script is to save a figure generated by matplotlib. Upon examination, the figure is saved and everything works fine. It's really strange then that the program crashes.
I added the -ggdb flag to my CFLAGS in /etc/make.conf python, wxpython, matplotlib and numpy with these new flags as advised here:
http://www.gentoo.org/proj/en/qa/backtraces.xml?style=printable
I also enabled creating a core dump file using the ulimit command.
After running my program, a file "core" is generated in the directory. Then I run gdb on it, however I don't really get any meaningful backtrace. This is what I get:
| Code: | $ gdb
GNU gdb (Gentoo 7.3.1 p2) 7.3.1
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.gentoo.org/>.
(gdb) core core
[New LWP 13235]
[New LWP 13245]
Core was generated by `python2.7 ./mpl_latex_plot_v2.py'.
Program terminated with signal 11, Segmentation fault.
#0 0x00007f03e4adce4a in ?? ()
(gdb) bt
#0 0x00007f03e4adce4a in ?? ()
#1 0x00007f03e2a20b10 in ?? ()
#2 0x0000000000000000 in ?? () |
Could someone point me out what I am doing wrong and how I could get more meaningful backtrace in order to find out where the segmentation fault is coming from in order to get rid of it.
Thanks a lot.
Last edited by jopeto on Sun Aug 26, 2012 2:09 pm; edited 1 time in total |
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Hu
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Joined: 06 Mar 2007
Posts: 21633
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| Posted: Sat Aug 25, 2012 2:54 pm Post subject: |
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| You linked to the backtrace guide, but you did not specify whether you also changed your FEATURES to prevent stripping. Debug symbols require quite a bit of space, so normally the package manager will strip the file to recover that space. As noted in the guide you referenced, you need FEATURES=splitdebug or FEATURES=nostrip to preserve those symbols. |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Sat Aug 25, 2012 8:39 pm Post subject: |
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Sorry, I guess I had not specified the features. Now this is what the relevant bits in my /etc/make.conf files look like:
| Code: | CFLAGS="-march=core2 -O2 -pipe -ggdb"
CXXFLAGS="${CFLAGS}"
MAKEOPTS="-j3"
FEATURES="-config-protect-if-modified splitdebug" |
I re-emerged python 2.7, wxpython, numpy and matplotlib. However when I run gdb on the core dump file, I get exactly the same output as before. Just ??.
One thing that I noticed is that in /usr/lib/debug, there is folder /usr/lib/debug/usr/bin and in it there is only one file python2.7.debug. There is no numpy, wxpython or matplotlib debug files, even though I re-emerged them after changing the flags and the FEATURES. |
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toralf
Developer
Joined: 01 Feb 2004
Posts: 3922
Location: Hamburg
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| Posted: Sat Aug 25, 2012 9:39 pm Post subject: |
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Well, beside that I've " -g -ggdb" you can exmine the core file with | Code: | | gdb --core=<core file> <path to the executable, eg. python 2.7> |
BTW you should consider default package CFLAGS in your make.conf | Code: | $ grep CFLAGS /etc/make.conf
CFLAGS="-O2 -march=native -pipe"
CXXFLAGS="${CFLAGS}"
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and then package specific flags like this : | Code: | $ cat /etc/portage/env/splitdebug
CFLAGS="${CFLAGS} -g -ggdb"
CXXFLAGS="${CFLAGS}"
FEATURES="splitdebug"
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and | Code: | $ grep splitdebug /etc/portage/package.env/misc | head -n 3
app-shells/bash splitdebug
<=dev-libs/glib-2.30.3 splitdebug notest
dev-libs/glib splitdebug
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Sun Aug 26, 2012 9:25 am Post subject: |
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Thanks a lot for your suggestion. So what I have now is the following:
In my /etc/make.conf file I have:
| Code: | CFLAGS="-march=core2 -O2 -pipe"
CXXFLAGS="${CFLAGS}"
MAKEOPTS="-j3"
FEATURES="-config-protect-if-modified" |
I also created a /etc/portage/env directory and put a file called debug.conf in it containing
| Code: | CFLAGS="${CFLAGS} -g -ggdb"
CXXFLAGS="${CFLAGS}"
FEATURES="splitdebug" |
Finally I created a /etc/portage/package.env file containing
| Code: | dev-lang/python:2.7 debug.conf
dev-python/wxpython debug.conf
dev-python/numpy debug.conf
dev-python/matplotlib debug.conf |
Then I re-emerged python 2.7, numpy, wxpython and matplotlib.
I ran my script again and a core dump file called "core" was generated. I ran the following commands
| Code: | $ eselect python list
Available Python interpreters:
[1] python2.7 *
[2] python3.2
$ which python
/usr/bin/python
$ gdb --core=core /usr/bin/python
GNU gdb (Gentoo 7.3.1 p2) 7.3.1
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.gentoo.org/>...
Reading symbols from /usr/bin/python...(no debugging symbols found)...done.
warning: core file may not match specified executable file.
[New LWP 25122]
[New LWP 25147]
Core was generated by `python2.7 ./mpl_latex_plot_v2.py'.
Program terminated with signal 11, Segmentation fault.
#0 0x00007f15533b5e4a in ?? ()
(gdb) bt
#0 0x00007f15533b5e4a in ?? ()
#1 0x00007f15512f9b10 in ?? ()
#2 0x0000000000000000 in ?? ()
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As you can see, once again no meaningful debug information was obtained. Any suggestions? |
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toralf
Developer
Joined: 01 Feb 2004
Posts: 3922
Location: Hamburg
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| Posted: Sun Aug 26, 2012 9:38 am Post subject: |
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| Well, specify /usr/bin/python2.7 because /usr/bin/python is only a symlink/wrapper to the actual python executeable. |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Sun Aug 26, 2012 1:14 pm Post subject: |
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| Thanks a lot, specifying python2.7 did it. Now I got a bit more detailed backtrace and I'll get in touch with the guys at the wxpython mail list. Thanks once again for your help. |
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toralf
Developer
Joined: 01 Feb 2004
Posts: 3922
Location: Hamburg
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| Posted: Sun Aug 26, 2012 2:07 pm Post subject: |
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| jopeto wrote: | | Thanks a lot, specifying python2.7 did it. Now I got a bit more detailed backtrace and I'll get in touch with the guys at the wxpython mail list. Thanks once again for your help. |
urw
BTW put a "[solved]" in front of the title of this thread - just for convenience. |
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