Curse of Nouvea. Must blacklist it then install Nvidia driver. Lots of web help on that. You need to be a geek for that.
Sent from my Verizon, Samsung Galaxy smartphone Get Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Mailing list for users of COOT Crystallographic Software <COOT@JISCMAIL.AC.UK> on behalf of David Bhella <david.bhe...@glasgow.ac.uk> Sent: Friday, May 26, 2023 8:56:23 AM To: COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> Subject: Re: stero/Mono&GPU Hi all There is another element to this I think - that NVIDIA have not supported 3D vision in their GPU drivers since 2019 - so you need to download and install a legacy driver I think 425 was the last release with 3Dvision support. I am away from my lab now so can’t check which version I am running on our CentOS 7 machine. D Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella On 26 May 2023, at 14:45, Colin Gauvin <co...@gauvin.id> wrote: We are running openSUSE Leap, but have also gotten hardware stereo working on other systems. Once you have a 3D vision capable GPU, display, and glasses kit, there are three tricky components I've discovered: The first is the Nvidia driver. I suspect the original emailer ran into issues here. There are two Nvidia drivers generally available: Nouvea, which is an open source driver, and Nvidia's own proprietary driver. You must use Nvidia's driver in my experience. Most distributions package this, but if not, it can be found on Nvidia's website. However, Nouveau likes to reinstall itself when updating some systems. I recommend using the package manager to lock the Nouveau after uninstalling it, so that it cannot be reinstalled. If nvidia-smi isn't working, this could be why. The next issue is the display manager/windowing system. This must be X11, not Wayland in my experience. A number of newer distributions such as Fedora use Wayland by default. Additionally, window compositing must be off. KDE desktop allows compositing to be switched off. Mate desktop + LightDM doesn't use compositing. I'm not sure about GNOME. 3rd is the X11 config file. X11 can have multiple configuration files. I can be tricky to figure out which one is actually in use. So if you make changes to one that don't work, start searching your system for others. Perhaps there's a rhyme or reason to this, but I've never checked. Make the changes to the Stereo type as listed on the SBGrid site (linked earlier in this thread). That should get hardware stereo working. Best, Colin Gauvin Cryo-EM Facility Assistant Manager Montana State University May 26, 2023 2:00:39 AM Dirk Kostrewa <dirk.kostr...@lrz.uni-muenchen.de>: Hi Kenneth & other 3D stereo users, what Kenneth writes overlaps with my experience, except for RHEL 8, which works fine in 3D stereo using the standard Gnome 3 desktop without any modifications (including composite). To my knowledge, this is the only distribution (and the underlying development version Fedora) which works in 3D stereo using the Gnome 3 shell. Upon switching to 3D stereo it takes about 1-2 seconds or so, until a message pops up telling you about enabling 3D stereo, and it also takes the same time to disable 3D stereo, again with a popup window. Interestingly, it appears to me that only the active 3D window switches to 3D stereo, not the whole desktop. How this is done by Fedora/RHEL 8 under the hood, I really do not know. The advantage of this window-switching is, that you can still use Coot's windows for scrolling through residues, rotamers, etc with clear readability. The disadvantage is, that you have to get the active 3D window into the foreground (by minimizing/maximizing or clicking its icon on the panel) to get rid of a sometimes flickering background. And you don't need to disable composite, neither in the xorg.conf file nor in the desktop settings. Best, Dirk On 25.05.23 17:49, Kenneth Satyshur wrote: Harware stereo. A complicated issue. I have been using it for a long time. The SGI computers used crystal eyes glasses and was displaying fine for the 90's, but went away with the end of SGI. So we switched to linux. For a while (2000's) 3D stereo was not useable, except on old SGI. Then Nvidia decided to take over the 3D gaming market with it's Nvidia 3D Vision system and GPUs. Wonderful, until they quit in 2019. Now all is WR, which is basically useless for molecular modelling density fitting. But I have gotten many a 3D hardware systems running on Linux. SBGrid has a web page explaining how to do this that still works. https://www.sbgrid.org/wiki/usage/stereo I don't know of any systems other than RHEL 7 and centos 7 that will do 3D. I have not tried them. Two issues need to be addressed: 1. hardware 2. Software 1. Hardware: You need an Nvidia graphics card that will do 3D stereo. I am using quadro cards, like K4000 and P5000. They will need an extra plugin connection to the card that will send a signal to a backplane 3DIN plus. This plug connects to the emitter back side. You only need this for Linux. Not needed for Windows. You also need a 3D ready 120 Hz monitor or better. However some gaming monitors will not work. And of course, the Nvidia 3D vision kit of glasses and emitter only sold on Ebay (used). 2. The OS should be Centos 7, Centos 8 will not work well. Also, the Gnome desktop no longer supports 3D Vision system. Use the mate Desktop. With the implementation of Wayland that replaces X11, gone are the 'no-compositing' options. VR uses composition, 3D Vision does not. This is changed in the xorg.conf file if you are still using X11. However, no-compositing will kill other graphics programs. I have not tried Ubuntu. Also, install the Nvidia drivers for your card. Section "Extensions" Option "COMPOSITE" "Disable" EndSection https://docs.nvidia.com/drive/drive_os_5.1.6.1L/nvvib_docs/index.html#page/DRIVE_OS_Linux_SDK_Development_Guide/Windows%20Systems/window_system_wayland.html if you want to find out about Wayland. and for the Geeks, check out the new Linix OS to replace Centos 7 since it is dead. https://wiki.archlinux.org/title/arch_compared_to_other_distributions I have checked the following programs for 3D stereo on my system (Centos 7, Mate desktop, K4000 Quadro, Acer GN24hl monitor) and they all do hardware stereo using Nvidia K4000 and 3D Vision system. coot 0.9.6 pymol all versions chimerax ver. 1.3 (Isolde does not do 3D stereo correctly). vmd 1.9.2 for 3D display of MD. I realize this is a lot of non-specific info, but if you contact me I can maybe walk you thru it. kas https://users.csc.calpoly.edu/~zwood/teaching/csc572/final11/rsomers/ https://pymolwiki.org/index.php/Stereo_3D_Display_Options https://wiki.uni-konstanz.de/ccp4/index.php?title=Stereo&mobileaction=toggle_view_desktop enough? Kenneth A. Satyshur, M.S., Ph.D. Scientist Emeritus From: College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 ________________________________ From: Mailing list for users of COOT Crystallographic Software <COOT@JISCMAIL.AC.UK><mailto:COOT@JISCMAIL.AC.UK> on behalf of Paul Emsley <pems...@mrc-lmb.cam.ac.uk><mailto:pems...@mrc-lmb.cam.ac.uk> Sent: Wednesday, May 24, 2023 11:47 PM To: COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK> <COOT@JISCMAIL.AC.UK><mailto:COOT@JISCMAIL.AC.UK> Subject: Re: stero/Mono&GPU On 12/05/2023 17:00, Gu Shaocheng wrote: > Hi, Hi. > Here is a GPU issue related to chimerax and coot (0.9.8) on the Linux system. OK... > To be able to call GPU in chimerax, I put the nvidia invoke in .bashrc file. I don't know what it means to call the GPU in ChimeraX. I don't know what the nvidia invoke is. Perhaps you are refering to an environment variable? > Chimerax works, In what way? What changes? > however, this will stop the working for coot to display structure at the > following view modes: `mono`, `side by side stereo`, and `side by side (wall > eyed)`. What do you mean by "stop the working"? That Coot doesn't start up? Or freezes? > It It? meaning Coot or the graphics card? > still works if I click 'hardware stereo' or 'Zalman Stereo' and I can see > it in `nvidia-smi`. "see it"? The graphics card? > Without GPU, each mode works fine. Without the graphics card, Coot will fall back to software rendering on the backend. Not many people these days think that that is "fine." > I wonder if we shouldn't run coot with GPU or if there are some potential > issues. > Does anyone have any idea about this? Thanks! For most people, Coot uses the GPU whether they like it or not. The advice I can give you is trite: use whatever gives you the best FPS. I'm not sure that I've been of much help. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT<http://www.jiscmail.ac.uk/COOT>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 -- ******************************************************* Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76998 E-mail: dirk.kostr...@lmu.de<mailto:dirk.kostr...@lmu.de> kostr...@genzentrum.lmu.de<mailto:kostr...@genzentrum.lmu.de> WWW: www.genzentrum.lmu.de<http://www.genzentrum.lmu.de> ******************************************************* ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
