Kernel unexpectedly dying; line of code: viz_cnmf.show(sidecar=True)

[santicolom]

Hi Kushal, I appreciate all the help so far. I'm still trying to get this code:

https://github.com/nel-lab/mesmerize-core/blob/master/notebooks/cnmfe.ipynb

to run properly with the demo data data_endoscope.tif that was provided.

With these fixes you recommended to me:

https://github.com/nel-lab/mesmerize-core/issues/252 https://github.com/nel-lab/mesmerize-core/issues/254

And this third fix that I applied because I was having the same error: https://github.com/nel-lab/mesmerize-core/issues/253

I did the developer install of fastplotlib and no longer have any error pop ups.

However near the end of the code:

Section: Visualize using mesmerize-viz

Code:

viz_cnmf.show(sidecar=True)

causes the kernel to unexpectedly die. I don't understand why, but I'd appreciate some more help. Thanks in advance.

[kushalkolar]

What hardware are you running on? Kernel crashes with fastplotlib are almost always insufficient hardware or driver issues.

[santicolom]

Device name LAPTOP-6NI4EHJA Processor AMD Ryzen 7 4800H with Radeon Graphics 2.90 GHz Installed RAM 16.0 GB (15.4 GB usable) Device ID 0F7F3A44-7E23-4D58-892B-D1264FCB6093 Product ID 00325-96677-49424-AAOEM System type 64-bit operating system, x64-based processor Pen and touch No pen or touch input is available for this display

Edition Windows 11 Home Version 22H2 Installed on ‎2/‎13/‎2023 OS build 22621.2715 Experience Windows Feature Experience Pack 1000.22677.1000.0

Sorry for the late response.

[kushalkolar]

My guess is that your iGPU only has 512MB of VRAM reserved for it, and when you call viz.show() for cnmf it runs out of VRAM. The mesviz visualizations can be quite large, you have two options:

• Increase the VRAM for the iGPU, there's usually a BIOS option for this. I would increase it to 2GB or 4GB.
• Use only one of the image data options instead of visualizing everything at once, viz_cnmf.show(image_data_options=["input"])

I would also close plots/image widgets after you are done with them.

[santicolom]

I tried increasing the VRAM in BIOS, but my laptop doesn't allow that kind of change.

Writing the above code I get the following response:

TypeError Traceback (most recent call last) Cell In[19], line 2 1 #viz_cnmf.show(sidecar=True) ----> 2 viz_cnmf.show(image_data_options=["input"])

TypeError: CNMFVizContainer.show() got an unexpected keyword argument 'image_data_options'

[kushalkolar]

Sorry that kwarg goes to creating the viz, to the cnmf.viz() call, and not show

[santicolom]

I tried it with "input" then with "rcm", kernel dies with both.

[kushalkolar]

Do you have a way to monitor VRAM usage and close anything else that might be using it? Anyways the only way you'll really be able to use it is by figuring out if you can increase the VRAM or use a different computer.

On Sat, Nov 25, 2023, 20:06 Santiago Colom @.***> wrote:

I tried it with "input" then with "rcm", kernel dies with both.

— Reply to this email directly, view it on GitHub https://github.com/nel-lab/mesmerize-core/issues/256#issuecomment-1826457807, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRHH6KQKFQQACK33UZDYGKIYPAVCNFSM6AAAAAA7TOPW2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRWGQ2TOOBQG4 . You are receiving this because you commented.Message ID: @.***>

[santicolom]

I'll try that, but most likely I'm gonna have to get a different computer to try this again because there doesn't appear to be a way of increasing VRAM from its default 512MB on my computer short of physical alterations. I appreciate the help so far, I'll let you know how it goes on a different system, but that won't be until a few days from now.

[kushalkolar]

Does anything get printed in the terminal that jupyter lab is running in? Anything about rust backtrace logs?

On Sat, Nov 25, 2023, 20:27 Santiago Colom @.***> wrote:

I'll try that, but most likely I'm gonna have to get a different computer to try this again because there doesn't appear to be a way of increasing VRAM from its default 512MB on my computer short of physical alterations. I appreciate the help so far, I'll let you know how it goes on a different system, but that won't be until a few days from now.

— Reply to this email directly, view it on GitHub https://github.com/nel-lab/mesmerize-core/issues/256#issuecomment-1826460939, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRDFTZWXEAF2AFIXXELYGKLJTAVCNFSM6AAAAAA7TOPW2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRWGQ3DAOJTHE . You are receiving this because you commented.Message ID: @.***>

[kushalkolar]

closing due to inactivity