Jupyter OSError: [Errno 122] Disk quota exceeded:

Question

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

Answer 1

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.