[Chimera-users] kill graphics windows after crash

[Dieter Blaas]

Hi Greg,

    thanks, I shall try!

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 06.10.2020 07:56, Greg Couch wrote:
> The next time Chimera won't go away, do a "ps -ef" in a terminal 
> window and find the process id, PID, for the Chimera Python process.  
> Then cat/more/less the contents of /proc/PID/wchan.  The wchan 
> contents indidcate where in the kernel the process is stuck waiting.  
> And then do some internet searches to figure out if it stuck on 
> accessing the disk, or network, or ....  It might be inconclusive, but 
> could be informative.
>
>     Good luck,
>
>     Greg
>
> On 10/5/2020 7:24 PM, 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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