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" <pems...@mrc-lmb.cam.ac.uk>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.
>
</pems...@mrc-lmb.cam.ac.uk>
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