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

Hi all,

I follow a tutorial that run on Jupyter Notebook:

    vae = scvi.model.SCVI(adata)

“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.

Do you have enough memory? Does pytorch work at all outside the context of this notebook?

1 Like

One sample work and another require upgrading MacOS to 12.3. You mean the Ram or hard drive storage?

My jupyter lab also says kernel died after running(python 3.9.12, centos7, 128gb ram, 500gb hdd):

sc.settings.verbosity = 3             # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.settings.set_figure_params(dpi=120, facecolor='white')

After comment out


notebook works but nothing printed out.

I run on GPU and don’t get that error anymore.

My server doesn’t have a GPU. GPU is required?

I am not sure but GPU worked in the cases I know.

As @adamgayoso hinted at, this is in most cases related to a memory issue. Can you ensure that memory availability can be ruled out?

1 Like