How to fix "the kernel appears to have died. It will restart automatically."?

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2.1 years ago

Chris ▴ 340

Hi all,

I follow this tutorial:

https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb

   scvi.model.SCVI.setup_anndata(adata)
    vae = scvi.model.SCVI(adata)
    vae.train()

"The kernel appears to have died. It will restart automatically."

GPU available: False, used: False
TPU available: False, using: 0 TPU cores
IPU available: False, using: 0 IPUs
HPU available: False, using: 0 HPUs
Epoch 1/400: 0%| | 0/400 [00:00<?, ?it/s]

This error seems because pytorch. I run 2 code samples to test pytorch, one is OK, another require upgrading MacOS to 12.3. What is wrong here? Thank you so much <3 .

scvi • 1.5k views

ADD COMMENT • link 2.1 years ago by Chris ▴ 340

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No guarantee that it is the cause, however, this behavior is consistent with you exceeding memory available. Are you using JupyterLab by any chance? It has a monitor of memory usage built in at the bottom of its interface so that you can have a better idea when you may be approaching that upper threshold as the code runs.

ADD REPLY • link 2.1 years ago by Wayne ★ 2.1k

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Yes, I run on Jupyter Notebook. I scroll to the bottom of the page and only see the last cell.

ADD REPLY • link 2.1 years ago by Chris ▴ 340

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