Auto start and nogui option causing segmentation fault?
Hello, I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode. I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options. chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC with many auto-start options on """
chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed
Starting extension 'Keyboard Shortcuts' failed Starting extension 'IDLE' failed
""" should I be adding a different flag or something when I start chimera via nogui? Thanks, Dan
Hi Daniel, Hmm, I’m not aware of other startup options to prevent such errors in nogui mode. It may simply be necessary to use a different preferences file ( you can have multiple ones and specify the one to use with the —preferences startup option ) without autostarts for running Chimera in nogui mode. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html> You could report this as a bug with Help… Report a Bug in the menu (GUI version, of course) or the address chimera-bugs@cgl.ucsf.edu . Even though the problem seems to be with the nogui version, the menu approach is useful because it automatically includes Chimera version and platform information. Either way, you could just paste in what you wrote in this message. Since I’m no help in this case, reporting a bug is good to make sure that the right people see it (although some are currently away, so it may be few days before there is any response), and to get it into our bug-tracking system. Sorry for the inconvenience, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2016, at 12:44 PM, Daniel P Farrell <danpf@uw.edu> wrote:
Hello,
I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode.
I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options.
chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC
with many auto-start options on """
chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed
Starting extension 'Keyboard Shortcuts' failed
Starting extension 'IDLE' failed
""" should I be adding a different flag or something when I start chimera via nogui?
Thanks, Dan
Yes, could you submit a bug report (as outlined by Elaine below) and attach your preferences file? If I set Model Panel to autostart, I get the “Starting extension 'Model Panel' failed” message, but no Python traceback. So it’s some other tool that’s the problem and your preferences file will allow me to determine the culprit. Your preferences file is /Users/danpf/.chimera/preferences. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 25, 2016, at 10:28 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Daniel, Hmm, I’m not aware of other startup options to prevent such errors in nogui mode. It may simply be necessary to use a different preferences file ( you can have multiple ones and specify the one to use with the —preferences startup option ) without autostarts for running Chimera in nogui mode. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html>
You could report this as a bug with Help… Report a Bug in the menu (GUI version, of course) or the address chimera-bugs@cgl.ucsf.edu . Even though the problem seems to be with the nogui version, the menu approach is useful because it automatically includes Chimera version and platform information. Either way, you could just paste in what you wrote in this message. Since I’m no help in this case, reporting a bug is good to make sure that the right people see it (although some are currently away, so it may be few days before there is any response), and to get it into our bug-tracking system.
Sorry for the inconvenience, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2016, at 12:44 PM, Daniel P Farrell <danpf@uw.edu> wrote:
Hello,
I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode.
I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options.
chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC
with many auto-start options on """
chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed
Starting extension 'Keyboard Shortcuts' failed
Starting extension 'IDLE' failed
""" should I be adding a different flag or something when I start chimera via nogui?
Thanks, Dan
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participants (3)
-
Daniel P Farrell -
Elaine Meng -
Eric Pettersen