{"id":909,"date":"2019-03-22T17:43:46","date_gmt":"2019-03-22T17:43:46","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=909"},"modified":"2024-11-27T14:02:13","modified_gmt":"2024-11-27T14:02:13","slug":"jupyter-notebook-2","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/jupyter-notebook-2\/","title":{"rendered":"Jupyter Notebook"},"content":{"rendered":"
This app replaces iPython notebook.
\nPlease use our Linux Virtual Desktop (nyx5,6,7) to access a running notebook through a web-browser.<\/div>\n

Overview<\/h2>\n

Jupyter Notebook<\/a> is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. We execute python commands and view the results in a web browser. The python commands execute remotely on the iCSF (where more memory and compute-power exists).<\/p>\n

Jupyter Notebook version 5.0.0 is installed on the iCSF as part of the Anaconda3 4.2.0<\/a> package. This runs Python 3.5.2.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions accessing this software. However you must have an account on the nyx5<\/code> \/ nyx6<\/code> \/ nyx7<\/code> virtual desktop server from which you then access the iCSF. Please see X2GO virtual desktop<\/a> for details. To request an account on nyx5,6,7 please email its-ri-team@manchester.ac.uk<\/a> (we will set up your account on all of the nyx servers).<\/p>\n

Set up procedure<\/h2>\n

The Jupyter Notebook software runs on one of the iCSF compute nodes (Aug 2024: All nodes are now 2TB nodes.) However, we do not<\/em> manually log in to the iCSF and run the Jupyter Notebook software directly. Instead we run a script on the nyx5\/nyx6\/nyx7<\/em> virtual desktop to manage the whole business of connecting to the iCSF and running the Jupyter Notebook software.<\/p>\n

Hence you must first log in to the nyx5 or nyx6 or nyx7 virtual desktop service<\/a> using the x2goclient<\/em> software. See links for details.<\/p>\n

Running the application<\/h2>\n

The following instructions assume you are logged in to the nyx5<\/em> virtual desktop (we use nyx5 in this example but you can also use nyx6 or nyx7).<\/p>\n

Launching the Jupyter Notebook on to the iCSF<\/h3>\n

Note: we use nyx7 in this example but you can also use nyx6 or nyx5.<\/p>\n

    \n
  1. On nyx7<\/strong>, open a shell window (e.g., using menu: Applications -> System Tools -> Terminal<\/em>)<\/li>\n
  2. In the terminal, run:\n
    # You run this command on nyx7 (or nyx6, or nyx5), not<\/em> the iCSF.<\/strong>\r\n# It will login to the iCSF and run a jupyter notebook.\r\njupyter-notebook-icsf\r\n<\/pre>\n<\/li>\n
  3. Enter your iCSF password when prompted:\n
    Connecting to the iCSF to start a Jupyter Notebook...\r\nusername<\/em>@incline256's password:  type your UoM IT password<\/strong>\r\n                                    (no characters will be displayed while you type)\r\n<\/pre>\n<\/li>\n
  4. Make a note of the URL address given to you – e.g.:\n
    http:\/\/localhost:7777\/?token=long-string-of-characters<\/em><\/pre>\n
    (the number 7777<\/code> may differ).<\/li>\n<\/ol>\n
    This will log you in to the iCSF (incline) and start the Jupyter Notebook server. Hence you will be asked for your iCSF password. Enter it when prompted.<\/p>\n
    For example, the complete output is:<\/p>\n
    [mabcxyz1@nyx7 ~]$ jupyter-notebook-icsf\r\n\r\n===================== Use the URL given here ====================\r\n\r\n 1. Enter your iCSF password when prompted below\r\n 2. On nyx7 please start firefox and browse to:\r\n\r\n           http:\/\/localhost:7777\/?token=<long string of characters>\r\n\r\n    (see below for the 'token' string to add to the above address)\r\n\r\nConnecting to the iCSF to start a Jupyter Notebook...\r\nmabcxyz1@incline256's password: <enter your iCSF password><\/strong>\r\n<\/pre>\n
    You will have been automatically logged in to the iCSF (on to one of the backend 2TB nodes). Notice the URL advertised to you:<\/p>\n
    http:\/\/localhost:7777\/?token=long-string-of-characters<\/em><\/strong><\/pre>\n
    The 7777<\/code> port number may be different in your output. You should make a note<\/strong> of the URL, particularly the port number and long string of random characters (which acts like a random password that only you can see – it prevents other people from access your notebook on the iCSF). We will access this URL in a web browser shortly.<\/p>\n
    You will see some output from the Jupyter Notebook server and then the message:<\/p>\n
    ======= ** IMPORTANT - YOU MUST DO THIS WHEN FINISHED WITH Jupyter ** =======\r\n Please use CTRL-C in this window to terminate Jupyter Notebook on incline21\r\n (PID 102924) ...\r\n<\/pre>\n
    We will use this when shutting down the server at the end of our session (see below).<\/p>\n
    View the Jupyter Notebook in a Web Browser on nyx7<\/h3>\n
    On the nyx7<\/em> virtual desktop:<\/p>\n
      \n
    1. Start firefox<\/code> (e.g., using menu: Applications -> Internet -> Firefox ESR<\/em>)<\/li>\n
    2. Now enter the following address in the browser address bar at the top:\n
      http:\/\/localhost:7777\/?token=long-string-of-characters<\/em><\/pre>\n
      where 7777\/?token=long-string-of-characters<\/em><\/code> and is the number and string reported to you earlier when you ran jupyter-notebook-icsf<\/code> in the command window. Your numbers may be different!<\/li>\n<\/ol>\n
      You should now see the Jupyter Notebook dashboard<\/em> in your web browser. This has connected to the iCSF backend node running the Jupyter Notebook.<\/p>\n
      Example Notebook<\/h3>\n
      Once you have connected to your notebook, try the following in your web-browser:<\/p>\n
        \n
      1. Select New -- Python3<\/code> to start a new python notebook.<\/li>\n
      2. Enter the following code in the first cell<\/em> (see image below):\n
        import os\r\nfile=os.getenv(\"JUPYTER_HOME\")+\"\/example_job\/mandelbrot.py\"\r\n%load $file\r\n<\/pre>\n
        \"Load<\/a><\/li>\n
      3. Press the Run<\/code> button twice<\/em> – firstly to load the mandelbrot.py<\/code> in to the notebook. Then secondly to execute the notebook code.<\/li>\n
      4. You should see a Mandelbrot fractal image in your web-browser. The code was executed in the batch job running on the compute node!
        \n        \"Mandelbrot<\/a><\/li>\n<\/ol>\n
        Stopping the Remote Notebook Server<\/h3>\n
        As mentioned above, when you have finished using the Jupyter Notebook on the iCSF you must close it down. Otherwise server processes may be left running on the iCSF backend nodes.<\/p>\n
          \n
        1. Press the ‘Logout’ button in the notebook’s web-page, or simply close your web-browser and, if you no longer want to connect back to the notebook<\/li>\n
        2. Now type CTRL-C<\/code> in the shell window that displayed the URL and message about pressing Ctrl+C<\/code>. It will report that it has shut down the server. You will be automatically logged out of the iCSF, leaving the shell window back at the nyx7<\/em> prompt:\n
          ======= ** IMPORTANT - YOU MUST DO THIS WHEN FINISHED WITH Jupyter ** =======\r\n Please use CTRL-C in this window to terminate Jupyter Notebook on incline21\r\n (PID 102924) ...\r\n\r\n....output while you were using the notebook in the web-browser....\r\n\r\n^C     <-- here we pressed CTRL-C<\/strong>\r\n[C 18:03:17.113 NotebookApp] received signal 15, stopping\r\n[I 18:03:17.198 NotebookApp] Shutting down kernels\r\n[I 18:03:17.800 NotebookApp] Kernel shutdown: 25521668-a97f-444b-8cac-e3718c8213c8\r\n\r\nTerminated Jupyter Notebook on incline21 (PID 102924).\r\nIf the command-prompt does not appear, press Ctrl+C again.\r\n\r\nConnection to incline closed.\r\nmabcxyz1@nyx7:~$ \r\n<\/pre>\n<\/li>\n
        3. That’s it, we’re back on nyx7 and the Jupyter Notebook server we were running on the iCSF has finished.<\/li>\n<\/ol>\n
          Further info<\/h2>\n