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@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@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@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@meduniwien.ac.at ------------------------------------------------------------------------
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