Hi, I just compiled graph-tool 2.2.17 from source under Ubuntu 12.10. When I enter the command 'import graph_tool' in the python interpreter everything appears to be working fine. Whoever when I create a python script (say test.py) containing the command 'import graph_tool' and attempt to run this script from the terminal (using the command python test.py) I get the error 'Segmentation fault (core dumped)'. I would really appreciate any help with this problem Regards, Padraig -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi, Is the seg fault gtk related ? (Maybe you could post the error message). I experienced such a seg fault, due to conflicting backends in matplotlib and graph_tool. A work around is to import matplotlib before graph_tool: import matplotlib.pyplot as plt import graph_tool.all as gt If I remove the first line, I get a seg fault with the following trace: /usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed import gobject._gobject /usr/lib/python2.7/dist-packages/gtk-2.0/gtk/__init__.py:40: Warning: specified class size for type `PyGtkGenericCellRenderer' is smaller than the parent type's `GtkCellRenderer' class size from gtk import _gtk /usr/lib/python2.7/dist-packages/gtk-2.0/gtk/__init__.py:40: Warning: g_type_get_qdata: assertion `node != NULL' failed from gtk import _gtk Erreur de segmentation (core dumped) Hope this helps, Cheers Guillaume Le 07/11/2012 16:46, Padraig a écrit :
Hi, I just compiled graph-tool 2.2.17 from source under Ubuntu 12.10. When I enter the command 'import graph_tool' in the python interpreter everything appears to be working fine.
Whoever when I create a python script (say test.py) containing the command 'import graph_tool' and attempt to run this script from the terminal (using the command python test.py) I get the error 'Segmentation fault (core dumped)'.
I would really appreciate any help with this problem Regards, Padraig
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Thanks Guillaume, No the the seg fault is not gtk related. The error message is the single line "Segmentation fault (core dumped)"; a script containing the single line "import graph_tool" generates this error. The strange thing is that any program I write appears to execute correctly but then throws this error as the program terminates. Padraig -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 11/08/2012 09:38 AM, Padraig wrote:
Thanks Guillaume, No the the seg fault is not gtk related. The error message is the single line "Segmentation fault (core dumped)"; a script containing the single line "import graph_tool" generates this error.
The strange thing is that any program I write appears to execute correctly but then throws this error as the program terminates.
I think you are seeing the same problem as http://projects.skewed.de/graph-tool/ticket/117 Would you please run your script in gdb and provide a stack trace of the crash? Also, which version of python and boost are you using? Cheers, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi the trace is below. I am running Python 2.7.3 and Boost 1.49. Yes it looks to same problem indeed. Padraig $ gdb python GNU gdb (GDB) 7.5-ubuntu Copyright (C) 2012 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-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /usr/bin/python...(no debugging symbols found)...done. (gdb) run test.py Starting program: /usr/bin/python test.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". Program received signal SIGSEGV, Segmentation fault. 0x00000000004b5d5a in ?? () (gdb) bt #0 0x00000000004b5d5a in ?? () #1 0x00000000004ef748 in ?? () #2 0x000000000048a57e in ?? () #3 0x00007ffff6f1f901 in ?? () from /lib/x86_64-linux-gnu/libc.so.6 #4 0x00007ffff6f1f985 in exit () from /lib/x86_64-linux-gnu/libc.so.6 #5 0x00007ffff6f05774 in __libc_start_main () from /lib/x86_64-linux-gnu/libc.so.6 #6 0x00000000004ce0ad in _start () -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi, On 11/08/2012 03:36 PM, Padraig wrote:
Hi the trace is below. I am running Python 2.7.3 and Boost 1.49. Yes it looks to same problem indeed. Padraig
$ gdb python GNU gdb (GDB) 7.5-ubuntu Copyright (C) 2012 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-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /usr/bin/python...(no debugging symbols found)...done. (gdb) run test.py Starting program: /usr/bin/python test.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Program received signal SIGSEGV, Segmentation fault. 0x00000000004b5d5a in ?? () (gdb) bt #0 0x00000000004b5d5a in ?? () #1 0x00000000004ef748 in ?? () #2 0x000000000048a57e in ?? () #3 0x00007ffff6f1f901 in ?? () from /lib/x86_64-linux-gnu/libc.so.6 #4 0x00007ffff6f1f985 in exit () from /lib/x86_64-linux-gnu/libc.so.6 #5 0x00007ffff6f05774 in __libc_start_main () from /lib/x86_64-linux-gnu/libc.so.6 #6 0x00000000004ce0ad in _start ()
Did you compile it yourself, or you used the ubuntu package? If you compiled it, what GCC did you use? I'm inclined to think this is a problem with openmp (GCC) + boost python. Since I cannot reproduce this problem, I cannot investigate myself. I would suggest different versions of GCC and Boost, and see if the problem also happens there. -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi, I compiled graph-tool myself but I'm just using the Ubuntu Boost package; I'm actually using the offical Ubuntu versions of Boost and GCC. Thanks -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 11/08/2012 04:32 PM, Padraig wrote:
Hi, I compiled graph-tool myself but I'm just using the Ubuntu Boost package; I'm actually using the offical Ubuntu versions of Boost and GCC. Thanks
Does the problem disappear if you disable OpenMP? Ubuntu provides several GCC versions. You could try some version lower than the default and see if you see any change. -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi I didn't pass the option "--enable-openmp" to the ./configure script; therefore I presume OpenMP is not enabled -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi, Could you please confirm if this still happens with the new 2.2.18 version? Cheers, Tiago On 11/08/2012 05:12 PM, Padraig wrote:
Hi I didn't pass the option "--enable-openmp" to the ./configure script; therefore I presume OpenMP is not enabled
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-- Tiago de Paula Peixoto <tiago@skewed.de>
Ah... I feel like there is some problem specific to that libc.so ... i feel like i've seen it somewhere before. On 13 November 2012 11:54, Tiago de Paula Peixoto <tiago@skewed.de> wrote:
Hi,
Could you please confirm if this still happens with the new 2.2.18 version?
Cheers, Tiago
On 11/08/2012 05:12 PM, Padraig wrote:
Hi I didn't pass the option "--enable-openmp" to the ./configure script; therefore I presume OpenMP is not enabled
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-- Tiago de Paula Peixoto <tiago@skewed.de>
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Hi, just tested this now and I can confirm that the problem still persists with the new 2.2.18 version. Regards -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
I upvote the idea that you should reinstall gcc. that .so file comes from there. it could be an incompatibility? On 17 November 2012 08:51, Padraig <padraig.corcoran@ucd.ie> wrote:
Hi, just tested this now and I can confirm that the problem still persists with the new 2.2.18 version. Regards
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Hi, This is just to inform that this has been fixed in the new git version. (see ticket #117, http://projects.skewed.de/graph-tool/ticket/117 ). Cheers, Tiago On 11/17/2012 02:51 PM, Padraig wrote:
Hi, just tested this now and I can confirm that the problem still persists with the new 2.2.18 version. Regards
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-- Tiago de Paula Peixoto <tiago@skewed.de>
participants (4)
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Guillaume Gay -
Padraig -
Ronnie Ghose -
Tiago de Paula Peixoto