Jupyter OSError: [Errno 122] Disk quota exceeded:
The problem was that the disk space quota allocated for Home was exceeded. Checked with:
du --si -s $HOME
As results, Jupyter could not write '/home/user/.local/share/jupyter/runtime/kernel-7fc2dae5-da71-4ce3-889f-de615073dd51.json' Had to clean up the home directory.
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Updated on September 18, 2022Comments
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I am running jupyter notebook on a server and accessing it using ssh tunnelling. I am having a Kernel error when trying to start jupyter.
Traceback (most recent call last): File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/web.py", line 1592, in _execute result = yield result File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1133, in run value = future.result() File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1141, in run yielded = self.gen.throw(*exc_info) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/notebook/services/sessions/handlers.py", line 73, in post type=mtype)) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1133, in run value = future.result() File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1141, in run yielded = self.gen.throw(*exc_info) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 79, in create_session kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1133, in run value = future.result() File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1141, in run yielded = self.gen.throw(*exc_info) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 92, in start_kernel_for_session self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 1133, in run value = future.result() File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/tornado/gen.py", line 326, in wrapper yielded = next(result) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/notebook/services/kernels/kernelmanager.py", line 160, in start_kernel super(MappingKernelManager, self).start_kernel(**kwargs) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel km.start_kernel(**kwargs) File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/jupyter_client/manager.py", line 240, in start_kernel self.write_connection_file() File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/jupyter_client/connect.py", line 472, in write_connection_file kernel_name=self.kernel_name File "/home/user/.conda/envs/bakbio/lib/python3.6/site-packages/jupyter_client/connect.py", line 137, in write_connection_file with open(fname, 'w') as f: OSError: [Errno 122] Disk quota exceeded: '/home/user/.local/share/jupyter/runtime/kernel-7fc2dae5-da71-4ce3-889f-de615073dd51.json'
The error message seems obvious but I don't know how to solve it. I tried to remove some heavy files from my account and relaunch jupyter but still same error. Also, this happens after trying some calculation requiring large memory. The generated file from the calculation (which has not complete) is just 2.8G but I am suspecting some cached files somewhere.
Configuration: Linux version 3.10.0-514.6.1.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) ) conda 4.5.11 jupyter notebook 5.7.2