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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Thu Oct 15 12:56:09 PDT 2020 

Dear Greg,

      as I stated, I moved the chimera windows to the bottom of the 
screen and finally to another workspace. A day later, chimera had 
closed. So I suspect that it is just a matter of time until it 
closes.... Something seems to very much retard its reaction to mouse 
clicks! I shall continue observing and use the 'Report a Bug' if it 
occurs again....

thanks again, 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 14.10.2020 08:12, Greg Couch wrote:
>
> 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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