Cannot get lock on nbsignatures.db on NFS mounts

[maahn]

First, thanks for sharing this great project!

I have trouble running voila on our server where the user directory are on an NFS mount. After reloading the notebooks a couple of times, I get:

ERROR:tornado.application:Uncaught exception GET / (10.173.82.189)
HTTPServerRequest(protocol='http', host='linux256:8866', method='GET', uri='/', version='HTTP/1.1', remote_ip='10.173.82.189')
Traceback (most recent call last):
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
    result = await result
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/voila/handler.py", line 49, in get
    notebook = yield self.load_notebook(notebook_path)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
    value = future.result()
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
    yielded = next(result)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/voila/handler.py", line 98, in load_notebook
    model = self.contents_manager.get(path=path)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/jupyter_server/services/contents/filemanager.py", line 387, in get
    model = self._notebook_model(path, content=content)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/jupyter_server/services/contents/filemanager.py", line 346, in _notebook_model
    self.mark_trusted_cells(nb, path)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/jupyter_server/services/contents/manager.py", line 503, in mark_trusted_cells
    trusted = self.notary.check_signature(nb)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/nbformat/sign.py", line 439, in check_signature
    return self.store.check_signature(signature, self.algorithm)
  File "/home/myuser/miniconda3/lib/python3.7/site-packages/nbformat/sign.py", line 232, in check_signature
    """, (algorithm, digest)).fetchone()
sqlite3.OperationalError: disk I/O error
ERROR:tornado.general:Could not open static file '/base/images/favicon.ico'
ERROR:tornado.general:Could not open static file '/style/style.min.css'
ERROR:tornado.access:500 GET / (10.173.82.189) 213.65ms

Looking at the code, it appears that voila has trouble with opening ~/.local/share/jupyter/nbsignatures.db
which has been an issue on NFS mounts for Jupyter before (e.g. jupyter/jupyter#174 (comment))

Forcing voila to use another data_dir with e.g. export JUPYTER_PATH=/tmp/jupyter didn't work.

Thanks

[jtpio]

Voila is built on top of Jupyter Server and most likely inherit this issue from it.

Is this still an issue with the latest version? Or have you found a solution in the meantime?

[maartenbreddels]

I'm hoping this is solved, but indeed, I don't think this is a voila issue.