running jupyter notebook Error: Kernel died

[fzhang988]

[E 22:46:08.468 remote_ikernel] Kernel died.
[I 22:46:08.853 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
WARNING:root:kernel 59e2d9fd-b056-45da-95cf-05e6543e657b restarted
[E 22:46:08.854 NotebookApp] KernelRestarter: restart callback <bound method ZMQChannelsHandler.on_kernel_restarted of ZMQChannelsHandler(59e2d9fd-b056-45da-95cf-05e6543e657b)> failed
Traceback (most recent call last):
File "/home/zhang/miniconda3/lib/python3.8/site-packages/jupyter_client/restarter.py", line 86, in _fire_callbacks
callback()
File "/home/zhang/miniconda3/lib/python3.8/site-packages/notebook/services/kernels/handlers.py", line 476, in on_kernel_restarted
self._send_status_message('restarting')
File "/home/zhang/miniconda3/lib/python3.8/site-packages/notebook/services/kernels/handlers.py", line 472, in _send_status_message
self.write_message(json.dumps(msg, default=date_default))
File "/home/zhang/miniconda3/lib/python3.8/site-packages/tornado/websocket.py", line 339, in write_message
raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
[I 22:46:08.976 remote_ikernel] Remote kernel version: 0.4.6.
[I 22:46:08.976 remote_ikernel] File location: /home/zhang/miniconda3/envs/scenic_protocol/lib/python3.6/site-packages/remote_ikernel/kernel.py.
[I 22:46:08.977 remote_ikernel] Launching kernel over SSH.
[I 22:46:08.977 remote_ikernel] Login command: 'ssh -o StrictHostKeyChecking=no hostname2'.
[I 22:46:08.996 remote_ikernel] Established connection; starting kernel.
[I 22:46:08.996 remote_ikernel] Remote working directory /home/zhang//Desktop/pySCENIC/notebooks.
[I 22:46:09.147 remote_ikernel] Running kernel command: 'source /home/zhang/miniconda3/etc/profile.d/conda.sh && conda activate scenic_protocol && /home/zhang/miniconda3/envs/scenic_protocol/bin/ipython3 kernel -f ./rik_kernel-59e2d9fd-b056-45da-95cf-05e6543e657b.json'.
[I 22:46:09.476 remote_ikernel] Setting up tunnels on ports: 60137, 48085, 52635, 41725, 47981.
[E 22:46:12.254 remote_ikernel] Kernel died.
[I 22:46:12.639 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
[I 22:46:12.760 remote_ikernel] Remote kernel version: 0.4.6.
[I 22:46:12.760 remote_ikernel] File location: /home/zhang/miniconda3/envs/scenic_protocol/lib/python3.6/site-packages/remote_ikernel/kernel.py.
[I 22:46:12.760 remote_ikernel] Launching kernel over SSH.
[I 22:46:12.760 remote_ikernel] Login command: 'ssh -o StrictHostKeyChecking=no hostname'.
[I 22:46:12.777 remote_ikernel] Established connection; starting kernel.
[I 22:46:12.777 remote_ikernel] Remote working directory ~/.
[I 22:46:12.928 remote_ikernel] Running kernel command: 'source /home/zhang/miniconda3/etc/profile.d/conda.sh && conda activate scenic_protocol && /home/zhang/miniconda3/envs/scenic_protocol/bin/ipython3 kernel -f ./rik_kernel-77cfb9ea-6645-42ed-a876-48a465519bf4.json'.
[I 22:46:13.259 remote_ikernel] Setting up tunnels on ports: 45899, 39335, 40115, 59567, 34567.
[E 22:46:14.482 remote_ikernel] Kernel died.

Why Kernel always died? Thanks,
Fan

[cflerin]

Hi @fzhang988 ,

It looks like you're trying to connect to a remote machine with pySCENIC installed in a conda environment. Your kernel command looks ok, but have you tried running it "manually"? From a terminal, ssh into your remote machine, and run your command (up to the ipython part):

source /home/zhang/miniconda3/etc/profile.d/conda.sh && conda activate scenic_protocol && /home/zhang/miniconda3/envs/scenic_protocol/bin/ipython3

If that gives you an error, it should help you track down what's going on.

[cflerin]

See #21 for some additional information on setting up remote and local kernels with singularity images.