When I try to start the ipython notebook from EPD's Canopy while not connected to the Internet, the notebook crashes before starting up.
This does not happen when connected to the net.
Any help would be most welcome.
The short crash dump follows next. The full dump from setting c.Application.verbose_crash=True in the config file can be found here https://gist.github.com/xaverm/6873969
Short dump
~>.Canopy/EPDenvironment/bin/ipython notebook
[NotebookApp] Using existing profile dir: u'/home/xuserx/.ipython/profile_default'
[NotebookApp] Serving notebooks from /home/xuserx
Traceback (most recent call last):
File ".Canopy/EPDenvironment/bin/ipython", line 10, in <module>
sys.exit(launch_new_instance())
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py", line 401, in launch_new_instance
app.initialize()
File "<string>", line 2, in initialize
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error
return method(app, *args, **kwargs)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py", line 313, in initialize
super(TerminalIPythonApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error
return method(app, *args, **kwargs)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/core/application.py", line 325, in initialize
self.parse_command_line(argv)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.py", line 308, in parse_command_line
return super(TerminalIPythonApp, self).parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error
return method(app, *args, **kwargs)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 420, in parse_command_line
return self.initialize_subcommand(subc, subargv)
File "<string>", line 2, in initialize_subcommand
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error
return method(app, *args, **kwargs)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 359, in initialize_subcommand
self.subapp.initialize(argv)
File "<string>", line 2, in initialize
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/config/application.py", line 84, in catch_config_error
return method(app, *args, **kwargs)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/frontend/html/notebook/notebookapp.py", line 532, in initialize
self.init_webapp()
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/IPython/frontend/html/notebook/notebookapp.py", line 450, in init_webapp
self.http_server.listen(port, self.ip)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/tornado/netutil.py", line 100, in listen
sockets = bind_sockets(port, address=address)
File "/home/xuserx/.Canopy/EPDenvironment/lib/python2.7/site-packages/tornado/netutil.py", line 248, in bind_sockets
0, flags)):
gaierror: [Errno -9] Address family for hostname not supported
This issue should be considerd closed: even after a complete Canopy reinstall & update, standalone ipython notebooks started from out of the directory generated by ~/Canopy/canopy_cli setup, as described on http://docs.enthought.com/canopy/configure/canopy-cli.html still do crash if the host is not connected to a network. However the ipython notebook started from .Canopy/Enthought/Canopy_64bit/User/bin/ipython now works also if disconnected from a network. That's ok. for me.
Related
Am trying to execute Jupyter notebook from command line. Am currently using the docker image provided in below link
https://hub.docker.com/r/jupyter/pyspark-notebook
When i try to execute below in command line it fails.
jupyter nbconvert --to notebook --ExecutePreprocessor.kernel_name=PySpark --ExecutePreprocessor.timeout=3600 --execute notebooks/sample-notebook.ipynb
Below is the error message
[NbConvertApp] Converting notebook notebooks/sample-notebook.ipynb to notebook
Traceback (most recent call last):
File "/opt/conda/bin/jupyter-nbconvert", line 11, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.7/site-packages/jupyter_core/application.py", line 270, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/traitlets/config/application.py", line 664, in launch_instance
app.start()
File "/opt/conda/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 340, in start
self.convert_notebooks()
File "/opt/conda/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook
output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook
output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
return self.from_file(f, resources=resources, **kw)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 197, in from_file
return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/exporters/notebook.py", line 32, in from_notebook_node
nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 139, in from_notebook_node
nb_copy, resources = self._preprocess(nb_copy, resources)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 316, in _preprocess
nbc, resc = preprocessor(nbc, resc)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__
return self.preprocess(nb, resources)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 403, in preprocess
with self.setup_preprocessor(nb, resources, km=km):
File "/opt/conda/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 345, in setup_preprocessor
self.km, self.kc = self.start_new_kernel(**kwargs)
File "/opt/conda/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 291, in start_new_kernel
km.start_kernel(extra_arguments=self.extra_arguments, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/jupyter_client/manager.py", line 301, in start_kernel
kernel_cmd, kw = self.pre_start_kernel(**kw)
File "/opt/conda/lib/python3.7/site-packages/jupyter_client/manager.py", line 254, in pre_start_kernel
kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
File "/opt/conda/lib/python3.7/site-packages/jupyter_client/manager.py", line 178, in format_kernel_cmd
cmd = self.kernel_spec.argv + extra_arguments
File "/opt/conda/lib/python3.7/site-packages/jupyter_client/manager.py", line 84, in kernel_spec
self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
File "/opt/conda/lib/python3.7/site-packages/jupyter_client/kernelspec.py", line 235, in get_kernel_spec
raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named PySpark
PATH looks like this, what am I doing wrong? Pywin32 and Pandoc are already installed using Windows MSI:
C:\Users\AliDesktop\Anaconda;C:\Users\AliDesktop\Anaconda\Scripts;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Program Files (x86)\Graphviz2.38\bin\;C:\Users\AliDesktop\AppData\Local\Pandoc\
I get this on trying to run a command I usually run:
ipython nbconvert --to latex --post PDF .ipynb
C:\Users\AliDesktop\Desktop\Magic Briefcase\School\1\1- Intro to Data Science\le
cture\Summaries\IPython Notebooks>ipython nbconvert --to latex --post PDF .ipynb
Below is my error traceback:
Traceback (most recent call last):
File "C:\Users\AliDesktop\Anaconda\lib\runpy.py", line 162, in _run_module_as_
main
"__main__", fname, loader, pkg_name)
File "C:\Users\AliDesktop\Anaconda\lib\runpy.py", line 72, in _run_code
exec code in run_globals
File "C:\Users\AliDesktop\Anaconda\Scripts\ipython.exe\__main__.py", line 9, i
n <module>
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\__init__.py", lin
e 120, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 573, in launch_instance
app.initialize(argv)
File "<string>", line 2, in initialize
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\terminal\ipapp.py
", line 321, in initialize
super(TerminalIPythonApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\core\application.
py", line 369, in initialize
self.parse_command_line(argv)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\terminal\ipapp.py
", line 316, in parse_command_line
return super(TerminalIPythonApp, self).parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 471, in parse_command_line
return self.initialize_subcommand(subc, subargv)
File "<string>", line 2, in initialize_subcommand
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 409, in initialize_subcommand
self.subapp.initialize(argv)
File "<string>", line 2, in initialize
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\nbconvert\nbconve
rtapp.py", line 211, in initialize
super(NbConvertApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\core\application.
py", line 369, in initialize
self.parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 495, in parse_command_line
self.update_config(config)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 394, in update_config
self.config = newconfig
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\utils\traitlets.p
y", line 445, in __set__
obj._notify_trait(self.name, old_value, new_value)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\utils\traitlets.p
y", line 602, in _notify_trait
c(name, old_value, new_value)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\applicatio
n.py", line 241, in _config_changed
SingletonConfigurable._config_changed(self, name, old, new)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\configurab
le.py", line 159, in _config_changed
self._load_config(new, traits=traits, section_names=section_names)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\config\configurab
le.py", line 143, in _load_config
setattr(self, name, deepcopy(config_value))
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\utils\traitlets.p
y", line 445, in __set__
obj._notify_trait(self.name, old_value, new_value)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\utils\traitlets.p
y", line 602, in _notify_trait
c(name, old_value, new_value)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\nbconvert\nbconve
rtapp.py", line 193, in _postprocessor_class_changed
self.postprocessor_factory = import_item(new)
File "C:\Users\AliDesktop\Anaconda\lib\site-packages\IPython\utils\importstrin
g.py", line 50, in import_item
return __import__(parts[0])
ImportError: No module named PDF
The options --to latex --post PDF have been replaced by --to pdf in IPython >= 3.0. So this should work:
ipython nbconvert --to pdf </path/to/notebook>
For further information see also issue #7973 on github.
When I run ipython notebook; I get "ImportError: IPython.html requires pyzmq >= 13" error message in console. I already run " pip install "ipython[notebook]" " but I can not run the notebook. Could you pls assist how to solve this issue.
C:\Python27\Scripts>ipython notebook
Traceback (most recent call last):
File "C:\Python27\lib\runpy.py", line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "C:\Python27\lib\runpy.py", line 72, in _run_code
exec code in run_globals
File "C:\Python27\Scripts\ipython.exe\__main__.py", line 9, in <module>
File "C:\Python27\lib\site-packages\IPython\__init__.py", line 120, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 573, in launch_instance app.initialize(argv)
File "<string>", line 2, in initialize
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Python27\lib\site-packages\IPython\terminal\ipapp.py", line 321, in initialize super(TerminalIPythonApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Python27\lib\site-packages\IPython\core\application.py", line 369, in initialize self.parse_command_line(argv)
File "C:\Python27\lib\site-packages\IPython\terminal\ipapp.py", line 316, in parse_command_line
return super(TerminalIPythonApp, self).parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 471, in parse_command_line
return self.initialize_subcommand(subc, subargv)
File "<string>", line 2, in initialize_subcommand
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 75, in catch_config_error
return method(app, *args, **kwargs)
File "C:\Python27\lib\site-packages\IPython\config\application.py", line 402, in initialize_subcommand
subapp = import_item(subapp)
File "C:\Python27\lib\site-packages\IPython\utils\importstring.py", line 42, in import_item
module = __import__(package, fromlist=[obj])
File "C:\Python27\lib\site-packages\IPython\html\notebookapp.py", line 29, in <module>
check_for_zmq('13', 'IPython.html')
File "C:\Python27\lib\site-packages\IPython\utils\zmqrelated.py", line 12, in check_for_zmq
raise ImportError("%s requires pyzmq >= %s"%(required_by,minimum_version))
ImportError: IPython.html requires pyzmq >= 13
Looks like you need the pyzmq package (version >= 13).
You can try installing it (or upgrading if need be) with :
pip install --upgrade pyzmq
These works for me ( win8 + anaconda 2.7.10 )
Uninstall zmq 4.0.4.
Install zmq 3.2.4.
pip uninstall ipython
pip install "ipython[all]"
pip uninstall pyzmq
pip install pyzmq
my ipython notebook functionality stop working.
If I do
ipython notebook
the console just hangs forever with no debug output.
I have already tried reinstalling ipython but no success.
Also, if I start normal ipython everything seems fine.
Does anybody have a clue how to solve this? I suspect some lock file is still there but how can I find out what is exactly going wrong?
also if I force interrupt I get the following stack trace
^C^CTraceback (most recent call last):
File "/home/lfiaschi/anaconda/bin/ipython", line 9, in <module>
load_entry_point('ipython==1.2.1', 'console_scripts', 'ipython')()
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/__init__.py", line 118, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 544, in launch_instance
app.initialize(argv)
File "<string>", line 2, in initialize
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 89, in catch_config_error
return method(app, *args, **kwargs)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 312, in initialize
super(TerminalIPythonApp, self).initialize(argv)
File "<string>", line 2, in initialize
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 89, in catch_config_error
return method(app, *args, **kwargs)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/core/application.py", line 373, in initialize
self.parse_command_line(argv)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 307, in parse_command_line
return super(TerminalIPythonApp, self).parse_command_line(argv)
File "<string>", line 2, in parse_command_line
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 89, in catch_config_error
return method(app, *args, **kwargs)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 474, in parse_command_line
return self.initialize_subcommand(subc, subargv)
File "<string>", line 2, in initialize_subcommand
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 89, in catch_config_error
return method(app, *args, **kwargs)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/config/application.py", line 405, in initialize_subcommand
subapp = import_item(subapp)
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/utils/importstring.py", line 42, in import_item
module = __import__(package, fromlist=[obj])
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/html/notebookapp.py", line 64, in <module>
from .services.kernels.kernelmanager import MappingKernelManager
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/html/services/kernels/kernelmanager.py", line 21, in <module>
from IPython.kernel.multikernelmanager import MultiKernelManager
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/kernel/__init__.py", line 6, in <module>
from .connect import *
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/kernel/connect.py", line 39, in <module>
from IPython.utils.localinterfaces import LOCALHOST
File "/home/lfiaschi/anaconda/lib/python2.7/site-packages/IPython/utils/localinterfaces.py", line 43, in <module>
PUBLIC_IPS = socket.gethostbyname_ex(socket.gethostname() + '.local')[2]
KeyboardInterrupt
I had the same problem in Linux/Ubuntu. This also hanged spyder.
Workaround for me:
(1) Look at host name of computer
cat /etc/hostname
which gives e.g. my-laptop
(2) Ensure that /etc/hosts contains the following entry
127.0.0.1 my-laptop my-laptop.local
because ipython looks for a 'local' extension too.
And fire up again ipython notebook or spyder. This worked for me for spyder, when it was hanging at:
PUBLIC_IPS = socket.gethostbyname_ex(socket.gethostname() + '.local')[2]
I was running ipython successfully on fedora 18 until now: I'm getting the following exception when trying to launch it:
Traceback (most recent call last):
File "/usr/bin/ipython", line 9, in <module>
load_entry_point('ipython==1.1.0', 'console_scripts', 'ipython')()
File "/usr/lib/python2.7/site-packages/IPython/__init__.py", line 118, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "/usr/lib/python2.7/site-packages/IPython/config/application.py", line 544, in launch_instance
app.initialize(argv)
File "<string>", line 2, in initialize
File "/usr/lib/python2.7/site-packages/IPython/config/application.py", line 89, in catch_config_error
return method(app, *args, **kwargs)
File "/usr/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 323, in initialize
self.init_shell()
File "/usr/lib/python2.7/site-packages/IPython/terminal/ipapp.py", line 339, in init_shell
ipython_dir=self.ipython_dir, user_ns=self.user_ns)
File "/usr/lib/python2.7/site-packages/IPython/config/configurable.py", line 349, in instance
inst = cls(*args, **kwargs)
File "/usr/lib/python2.7/site-packages/IPython/terminal/interactiveshell.py", line 320, in __init__
**kwargs
File "/usr/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 456, in __init__
self.init_history()
File "/usr/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 1487, in init_history
self.history_manager = HistoryManager(shell=self, parent=self)
File "/usr/lib/python2.7/site-packages/IPython/core/history.py", line 481, in __init__
self.new_session()
File "<string>", line 2, in new_session
File "/usr/lib/python2.7/site-packages/IPython/core/history.py", line 65, in needs_sqlite
return f(self, *a, **kw)
File "/usr/lib/python2.7/site-packages/IPython/core/history.py", line 500, in new_session
self.session_number = cur.lastrowid
OperationalError: disk I/O error
If you suspect this is an IPython bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev#scipy.org
You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.
Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
c.Application.verbose_crash=True
I tried to upgrade ipython to the latest version using pip, which did not help. Any solution or workaround is very much welcomed.
IPython store history in a profile generally in ~/.ipython/profile_default/history.sqlite. There seem to be a disk error reading/writting to it.
Check the permissions of the file/folders, if necessary delete the file.
I solved it by set c.NotebookNotary.db_file = u':memory:' in jupyter configure file ~/.jupyter/jupyter_notebook_config.py