Re: [COOT] stero/Mono

[吴飞]

Hi Paul,

Please let me clarify my question.  

1. system and software situation:
1.1 My OS is "Ubuntu 22.04.2 LTS x86_64" (Kernel: 5.19.0-41-generic). 
1.2 And my computer has a "GPU: NVIDIA GeForce GTX 1650 Mobile / Max-Q". and I 
installed nvidia-driver-530.
1.3 I am running Coot 0.9.8 EL.

2. issue
1.1 if I launch coot normally, coot can display pdb structure. but it will say 
"WARNING:: Can't enable stereo visual - falling back" if I click "hardware 
stereo". 
1.1.1 In this case, if I type `nvidia-smi`, I won't see coot's PID here. 

1.2 Now, I launch coot via `__GLX_VENDOR_LIBRARY_NAME=nvidia coot`. I can open 
coot and see its interface. but the interface for displaying is very tiny and 
don't show pdb structure. Then, I click "Hardware Stereo", coot says "WARNING:: 
Can't enable stereo visual - falling back", but now it can display structure. 
However, if then I click "Mono", it will say "INFO:: switch to mono_mode 
succeeded" and the displaying will freezing and no reaction to mouse operation. 
1.2.1 In this case, if I type `nvidia-smi`, I can see coot-bin PID here. but it 
only use 1Mib GPU memory.
{0   N/A  N/A 89540  G   .../cryoem/coot/0.9.8/libexec/coot-bin
1MiB }

1.3 about chimeraX. this is not important to coot's question, but maybe give 
some reference to understand the issue in coot. 
1.3.1 if I launch chimeraX directly, it can display but it will be slow and I 
don't see its PID in `nvidia-smi`.
1.3.2 if I launch it with `__GLX_VENDOR_LIBRARY_NAME=nvidia`, its displaying 
will become fast and I can see its PID in `nvidia-smi`.

1.4 a similar displaying issue related graphic card happens in coot 1.0 in my 
computer
1.4.1 it happens in ccp4 compiled version;
1.4.2 it happens in a version I compiled from scratch.
1.4.2 the issue related coot 1.0 has been reported in github 
(https://github.com/pemsley/coot/issues/64).

Lastly, thanks for your answer and a lot of reply under this topic.

Best wishes,
Gu Sahocheng.


"Paul Emsley" wrote:
 
 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.







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Re: [COOT] stero/Mono

[Dirk Kostrewa]

Hi David,

On 26.05.23 15:56, David Bhella wrote:

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.


this applies only for Windows 3D stereo. For Linux using Nvidia Quadro 
graphics cards and quad-buffered 3D stereo, you can still use the 
current Nvidia graphics driver (see here 
).


Best,

Dirk



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 ofGlasgow Centre for Virus Research
Director - Scottish Centre forMacromolecular 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  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 
:


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 

Re: [COOT] stero/Mono

[Kenneth Satyshur]

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

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of David Bhella 
Sent: Friday, May 26, 2023 8:56:23 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: stero/Mono

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  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 :

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 

Re: [COOT] stero/Mono

[David Bhella]

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  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 :

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 

Re: [COOT] stero/Mono

[Colin Gauvin]

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 :

> 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         

Re: [COOT] stero/Mono

[Dirk Kostrewa]

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=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 
 on behalf of Paul Emsley 

*Sent:* Wednesday, May 24, 2023 11:47 PM
*To:* COOT@JISCMAIL.AC.UK 
*Subject:* Re: stero/Mono
On 12/05/2023 17:00, Gu Shaocheng wrote:
> Hi,

Hi.

> Here 

Re: [COOT] stero/Mono

[Kenneth Satyshur]

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=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 
 on behalf of Paul Emsley 
Sent: Wednesday, May 24, 2023 11:47 PM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: stero/Mono

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.



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Re: [COOT] stero/Mono

[Paul Emsley]

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.



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

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[COOT] stero/Mono

[Gu Shaocheng]

Hi,

Here is a GPU issue related to chimerax and coot (0.9.8) on the Linux system. 
To be able to call GPU in chimerax, I put the nvidia invoke in .bashrc file.
Chimerax works, 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)`.
It still works if I click 'hardware stereo' or 'Zalman Stereo' and I can see it 
in `nvidia-smi`.
Without GPU, each mode works 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!

All the best,
Shaocheng



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

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