Hello Shasha,

My bad, I suggested this solution because I knew it worked for compute jobs, but I had not tried it with ChimeraX when I sent my email. I just tried now, and I observe the same behavior that you describe: ChimeraX uses the GPU connected to the monitor, no matter what environment variable I define before starting it (with ChimeraX 1.1 on CentOS 8.1).

I hope the workaround of choosing which GPU gets used by your compute jobs will be enough for you.

Cheers,

Guillaume


On 24 Nov 2020, at 18:21, Shasha Feng <shaalltime@gmail.com> wrote:

Hi Guillaume, and Eric

Thanks for the tip. The temporary assignment of visiable GPU devices is exactly what I want to get. Though it looks like the recipe of using 'CUDA_VISIBLE_DEVICES=1' does not work at least on my ubuntu 20.04 with chimerax 1.0. I also tried Eric's suggestion just now. 

sf@sf-MS-7C35:~$ echo $CUDA_VISIBLE_DEVICES

sf@sf-MS-7C35:~$ export CUDA_VISIBLE_DEVICES=1
sf@sf-MS-7C35:~$ echo $CUDA_VISIBLE_DEVICES
1
sf@sf-MS-7C35:~$ chimerax &
[1] 673010
sf@sf-MS-7C35:~$ nvidia-smi
Tue Nov 24 12:09:28 2020      
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 450.66       Driver Version: 450.66       CUDA Version: 11.0     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  GeForce RTX 207...  Off  | 00000000:2D:00.0  On |                  N/A |
| 60%   74C    P2   191W / 215W |    763MiB /  7974MiB |     99%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  GeForce RTX 207...  Off  | 00000000:2E:00.0 Off |                  N/A |
|  0%   34C    P8    14W / 215W |     14MiB /  7982MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|    0   N/A  N/A      1343      G   /usr/lib/xorg/Xorg                 35MiB |
|    0   N/A  N/A      2338      G   /usr/lib/xorg/Xorg                174MiB |
|    0   N/A  N/A      2463      G   /usr/bin/gnome-shell              233MiB |
|    0   N/A  N/A    671633      G   ...AAAAAAAAA= --shared-files       45MiB |
|    0   N/A  N/A    672504      C   /opt/conda/bin/python             229MiB |
|    0   N/A  N/A    673010      G   chimerax                           33MiB |
|    1   N/A  N/A      1343      G   /usr/lib/xorg/Xorg                  4MiB |
|    1   N/A  N/A      2338      G   /usr/lib/xorg/Xorg                  4MiB |
+-----------------------------------------------------------------------------+

After setting the environment variable and running chimerax in the same session, it still runs on GPU 0. 
I also tried a recipe that defines 
"export NVIDIA_VISIBLE_DEVICES=1,
export CUDA_VISIBLE_DEVICES=0" shared here [https://stackoverflow.com/a/58445444]. It does not work either.  

To ChimeraX developers,
I wonder how ChimeraX is exposed to CUDA. I have basis in CUDA computing and using CUDA in Python. If you can give some clues, that would be great.

Best,
Shasha

On Tue, Nov 24, 2020 at 12:18 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
To supplement Guilaume's very helpful answer, you could make an alias to reduce the typing involved, and you could put the alias in your shell startup file.  For the bash shell, the syntax for making an alias named 'cx' for the command would be:

alias cx="CUDA_VISIBLE_DEVICES=1 chimerax"

Other shells have similar (but not necessarily identical) syntaxes.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Nov 24, 2020, at 12:09 AM, Guillaume Gaullier <guillaume@gaullier.org> wrote:

Hello,

You can restrict which of your GPUs ChimeraX will be able to detect by starting it from the shell like so:

CUDA_VISIBLE_DEVICES=1 chimerax

replace 1 with the device number you want, this is the same one as reported by nvidia-smi. This will work until you close ChimeraX, next time you run it you still need to add the environment variable before the "chimerax" command.

You can also make this environment variable stay around until you close the shell session like so:

export CUDA_VISIBLE_DEVICES=1

then you can open ChimeraX from the same shell session, close it, and reopen with only the "chimerax" command and it should still only see the GPU you indicated.

When you close and restart your shell, you will have to export the environment variable again. I don’t recommend adding the export to your ~/.bashrc or other shell initialization script, because then all your shell sessions will have this environment variable set, so all the commands you run will only see this GPU, which is probably not what you want. It is less likely to get in your way down the road if you only set this environment variable for the duration of a shell you opened specifically to run ChimeraX from.

I hope this helps,

Guillaume


On 24 Nov 2020, at 01:51, Shasha Feng <shaalltime@gmail.com> wrote:

Hi Tom,

Sorry about not clarifying my operating system. I am using ubuntu 20.04 with two NVIDIA GPU cards. 
Do I need to change OpenGL setting or reconfigure the nvidia setting? 

Thanks,
Shasha



On Mon, Nov 23, 2020 at 6:58 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Shasta,

ChimeraX has no way to select which GPU it uses.   The operating system or opengl driver decides.  You didn't mention which operating system you are using.  Here is an example of how to set the default OpenGL GPU in Windows.


  Tom


On Nov 23, 2020, at 2:38 PM, Shasha Feng <shaalltime@gmail.com> wrote:

Hi,

Is there any way to specify which GPU device for ChimeraX to run on? Currently, it uses the default GPU 0, which can disturb the existing jobs. Thanks.

Best,
Shasha

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