kill graphics windows after crash
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 ------------------------------------------------------------------------
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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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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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 ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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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 ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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 ------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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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@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@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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_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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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@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@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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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@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@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@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
-----------------------------------------------------------------------
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Hi Dieter, I guess next time look for "python" in the process table and also note its "state" column (titled "S"). You may not be able to kill the process if its state is "Z" (zombie process) or "U" (uninterruptible wait). Regardless, try to kill it with "kill -s KILL process_id". --Eric
On Oct 15, 2020, at 12:56 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
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@meduniwien.ac.at <mailto:dieter.blaas@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@meduniwien.ac.at <mailto:dieter.blaas@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@meduniwien.ac.at <mailto: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> <mailto: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> <mailto: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 <mailto:dieter.blaas@meduniwien.ac.at> > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >
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participants (4)
-
Dieter Blaas -
Eric Pettersen -
Greg Couch -
Tom Goddard