diff --git a/CHANGES.rst b/CHANGES.rst index b54ac3d..e3fe44b 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -6,7 +6,7 @@ Changelog for Jupyter-O2 **Removed:** -* This version removes compatibility with Python 2.7, +- This version removes compatibility with Python 2.7, which has not been supported since version 1.0.2. **Improvements:** diff --git a/README.rst b/README.rst index 7ba7f1b..4b955a0 100644 --- a/README.rst +++ b/README.rst @@ -26,13 +26,13 @@ Next, on your local machine: Install Jupyter-O2. -.. code-block:: console +.. code-block:: bash pip install jupyter-o2 Then, generate the config file. -.. code-block:: console +.. code-block:: bash jupyter-o2 --generate-config @@ -40,7 +40,7 @@ Follow the printed path to ``jupyter-o2.cfg`` and edit according to its instruct ``DEFAULT_USER`` and ``INIT_JUPYTER_COMMANDS`` fields. You may copy this file to any of the locations listed by ``jupyter-o2 --paths`` if you wish. -Make sure you have X11 forwarding active (e.g. install `XQuartz `_ if on a Mac). +Make sure you have X11 forwarding active (install `XQuartz `_ if on a Mac). For more info on setting up Jupyter and troubleshooting Jupyter-O2, see the `jupyter-o2 tips`_. @@ -50,7 +50,7 @@ Usage ------------------------------ Jupyter-O2 should be run locally using the following command format: -.. code-block:: console +.. code-block:: bash jupyter-o2 [subcommand] @@ -62,7 +62,7 @@ on the `O2 wiki `_. Note that if Jupyter is installed on your machine, Jupyter-O2 can also be run as a Jupyter subcommand: -.. code-block:: console +.. code-block:: bash jupyter o2 lab diff --git a/jupyter_o2_tips.rst b/jupyter_o2_tips.rst index d6847f3..3545407 100644 --- a/jupyter_o2_tips.rst +++ b/jupyter_o2_tips.rst @@ -2,6 +2,54 @@ Jupyter-O2 tips =============== +-------------------------------------------------------------------------------------------------------------------- +Troubleshooting +-------------------------------------------------------------------------------------------------------------------- + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +X11 error / missing DISPLAY variable +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +If you see ``srun: error: x11: no local DISPLAY defined``, +``No DISPLAY variable set``, or similar, you probably need to +install or reinstall `XQuartz `__. + +To test outside of Jupyter-O2, log in to the server with ``ssh -X`` +and check your DISPLAY using ``echo $DISPLAY``. +There should be a string printed in response. + +A possible alternative is to run Jupyter-O2 with the +``-Y`` argument to enable trusted X11 forwarding (less secure). + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +SSH error: pxssh error: could not synchronize with original prompt +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +If you are not on the HMS network or using the HMS VPN, +you will need to tell Jupyter-O2 use two-factor authentication +with the arguments ``--2fa --2fa-code 1``. + +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +nbsignatures.db +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +If Jupyter hangs when opening notebooks for the first time in any +session, and the console shows error messages such as: + +.. code-block:: + + > The signatures database cannot be opened; maybe it is corrupted or encrypted. + > Failed commiting signatures database to disk. + +Disabling Jupyter's signatures database may be the best option, since there is +no non-networked file system shared between all the interactive compute +nodes. + +1. Enter an interactive session and generate a notebook config using + ``jupyter notebook --generate-config`` +2. In ``~/.jupyter/jupyter_notebook_config.py`` set + ``c.NotebookNotary.db_file = ':memory:'`` + -------------------------------------------------------------------------------------------------------------------- Useful Jupyter add-ons -------------------------------------------------------------------------------------------------------------------- @@ -56,51 +104,3 @@ JupyterLab is now JupyterLab offers a more complete environment than Jupyter Notebook. With tabs for notebooks, terminals, consoles, text editors, and an integrated file browser, you could run almost anything you need on O2 from a single browser window. - --------------------------------------------------------------------------------------------------------------------- -Troubleshooting --------------------------------------------------------------------------------------------------------------------- - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -X11 error / missing DISPLAY variable -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -If you see ``srun: error: x11: no local DISPLAY defined``, -``No DISPLAY variable set``, or similar, you probably need to -install or reinstall `XQuartz `__. - -To test outside of Jupyter-O2, log in to the server with ``ssh -X`` -and check your DISPLAY using ``echo $DISPLAY``. -There should be a string printed in response. - -A possible alternative is to run Jupyter-O2 with the -``-Y`` argument to enable trusted X11 forwarding (less secure). - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -SSH error: pxssh error: could not synchronize with original prompt -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -If you are not on the HMS network or using the HMS VPN, -you will need to tell Jupyter-O2 use two-factor authentication -with the arguments ``--2fa --2fa-code 1``. - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -nbsignatures.db -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -If Jupyter hangs when opening notebooks for the first time in any -session, and the console shows error messages such as: - -.. code-block:: - - > The signatures database cannot be opened; maybe it is corrupted or encrypted. - > Failed commiting signatures database to disk. - -Disabling Jupyter's signatures database may be the best option, since there is -no non-networked file system shared between all the interactive compute -nodes. - -1. Enter an interactive session and generate a notebook config using - ``jupyter notebook --generate-config`` -2. In ``~/.jupyter/jupyter_notebook_config.py`` set - ``c.NotebookNotary.db_file = ':memory:'``