[Chimera-users] kill graphics windows after crash: it happend again

[Greg Couch]

Chimera will show up as "python" in the process table.  That's one of 
the fixes we made with ChimeraX, it shows up as ChimeraX. If you haven't 
done so already, when running Chimera, please use the Help / Report a 
Bug... dialog so we have a record of how your current system is 
configured (version of Linux, graphics driver version, etc.).  Are you 
still running Chimera remotely using VirtualGL?  If so, please state 
that in the description.

     Thanks,

     Greg

On 10/13/2020 10:46 PM, Dieter Blaas wrote:
> Hi,
>
>     it happened again: after the message that the loading of a map was 
> very slow chimera got stuck and I cannot get rid of its windows. If I 
> open something else it overlays the chimera windows. ps -ealf|grep 
> chimera just shows me a single process, namely the one of ps. Please 
> see attached screenshots! For the moment I can push the chimera 
> windows out of view but I cannot close them. I possibly have to reboot 
> again....
>
> thanks for hints, bw Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: dieter.blaas at meduniwien.ac.at
> ------------------------------------------------------------------------
>
> On 06.10.2020 04:24, Dieter Blaas wrote:
>> Dear Tom and Eric,
>>
>>      thank you! In the meantime I finally decided to reboot! The 
>> situation is difficult to reproduce but happens once within several 
>> months either because of a very slow network (when we experience 
>> general problems with the server) or because there is something wrong 
>> in a saved and then modified session file. However, I cannot exclude 
>> that the cause is something else! Fact is that I then cannot close 
>> any of the chimera windows, they simply stay open despite having 
>> killed all related processes.
>>
>> Could it be caused from working remotely over VNC? But when 
>> restarting the VNC server and then restarting Chimera it usually 
>> happens again! When I observe it next time I'll try "kill -s KILL 
>> process_id" and also take screen shots. As I am the only user 
>> rebooting is not a problem!
>>
>> best, Dieter
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Mobile: 0043 699 1942 1659
>> e-mail: dieter.blaas at meduniwien.ac.at
>> ------------------------------------------------------------------------
>>
>> On 05.10.2020 20:58, Tom Goddard wrote:
>>> Hi Dieter,
>>>
>>>    I am curious what you are using in Chimera that uses the network 
>>> when you have to kill it?  I tried fetching a large EM map (10860, 
>>> ~500 Mbytes) from EMDB with File / Fetch by ID on Mac, then I turned 
>>> off my wifi part way through and tried ctrl-C in the shell where I 
>>> had started Chimera 1.14.  One try it exited the program, and the 
>>> second try it gave a keyboard interrupt message and Chimera was no 
>>> longer hung.  If I left my wifi on then the stop button in the lower 
>>> left corner of the Chimera window at the front of the status 
>>> messages successfully stopped the download.  But if I disconnected 
>>> the wifi, that stop button didn't work.
>>>
>>>    Maybe you are on Linux or maybe Chimera is hung on some web 
>>> service you are using like BLAST....
>>>
>>>     Tom
>>>
>>>
>>>> On Oct 5, 2020, at 11:30 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>>>
>>>> Hi Dieter,
>>>>     Instead of "kill process_id" try "kill -s KILL process_id".
>>>>
>>>> --Eric
>>>>
>>>>     Eric Pettersen
>>>>     UCSF Computer Graphics Lab
>>>>
>>>>> On Oct 4, 2020, at 9:05 AM, Dieter Blaas 
>>>>> <dieter.blaas at meduniwien.ac.at> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>     please forgive me when this question is not directly related 
>>>>> to Chimera: Sometimes Chimera becomes unresponsive because of a 
>>>>> slow network connection. When I then try exiting it or killing it 
>>>>> with <ctrl> c from the terminal I used to start it or killing the 
>>>>> chimera-related process as shown with ps -ealf|grep UCSF or grep 
>>>>> chimera the chimera windows remain and I cannot remove them. Any 
>>>>> way of doing so?
>>>>>
>>>>> Thanks for hints, best, Dieter
>>>>>
>>>>> ----------------------------------------------------------------------- 
>>>>>
>>>>> Dieter Blaas,
>>>>> Max Perutz Labortories
>>>>> Medical University of Vienna,
>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>> Dr. Bohr Gasse 9/3,
>>>>> A-1030 Vienna, Austria,
>>>>> Tel: 0043 1 4277 61630,
>>>>> Mobile: 0043 699 1942 1659
>>>>> e-mail: dieter.blaas at meduniwien.ac.at
>>>>> ------------------------------------------------------------------------ 
>>>>>
>>>>>
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