{"id":436,"date":"2014-07-11T11:20:34","date_gmt":"2014-07-11T11:20:34","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=436"},"modified":"2019-03-22T17:21:10","modified_gmt":"2019-03-22T17:21:10","slug":"ipython-notebook","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/ipython-notebook\/","title":{"rendered":"IPython Notebook"},"content":{"rendered":"\n\n
This app is no longer available.
You should use jupyter notebook instead.<\/td>\n<\/tr>\n\n

Overview<\/h2>\n

IPython 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

IPython version 1.1.0 is installed on the iCSF as part of the Anaconda Python 1.9.2<\/a> package. This runs Python 2.7.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions accessing this software. However you must have an account on the nyx3<\/code> or nyx4<\/code> virtual desktop server from which you then access the iCSF. Please see X2GO virtual desktop<\/a> for details. To request an account on nyx3\/nyx4 please email its-ri-team@manchester.ac.uk<\/a>.<\/p>\n

Set up procedure<\/h2>\n

The IPython Notebook software runs on one of the iCSF compute nodes. However, we do not manually log in to the iCSF and run the IPython Notebook software. Instead we run a script on the nyx3\/nyx4<\/em> virtual desktop to manage the whole business of connecting to the iCSF and running the IPython software.<\/p>\n

Hence you must first log in to the nyx3 or nyx4 virtual desktop service<\/a> using the x2goclient<\/em> software. See links for details.<\/p>\n

(The RI Team are developing a method to allow you to do this direct from your desktop but for now we must use the nyx3\/nyx4 virtual desktop).<\/p>\n

Running the application<\/h2>\n

The following instructions assume you are logged in to the nyx3<\/em> virtual desktop (we use nyx3 in this example but you can also use nyx4).<\/p>\n

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

Note: we use nyx3 in this example but you can also use nyx4.<\/p>\n

    \n
  1. On nyx3, open a shell window (e.g., using menu: Applications -> System Tools -> Terminal<\/em>)<\/li>\n
  2. In the terminal, run:\n
    \r\nipython-notebook         # Add --highmem to use iCSF 256GB node<\/pre>\n<\/li>\n
  3. Enter your iCSF password when prompted<\/li>\n
  4. Make a note of the URL address given to you – e.g.: http:\/\/localhost:7777<\/code> (the number at the end may differ).<\/li>\n<\/ol>\n
    This will log you in to the iCSF (incline) and start the IPython 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
    \r\n[mabcxyz1@nyx3 ~]$ ipython-notebook \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 nyx3 please start iceweasel and browse to:\r\n\r\n           http:\/\/localhost:7777\r\n\r\nConnecting to the iCSF to start an iPython Notebook...\r\nmabcxyz1@incline'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 nodes). Notice the URL advertised to you:<\/p>\n
    http:\/\/localhost:7777<\/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. We will access this URL in a web browser shortly.<\/p>\n
    You will see some output from the IPython Notebook server and then the message:<\/p>\n
    \r\n======= ** IMPORTANT - YOU MUST DO THIS WHEN FINISHED WITH IPython ** =======\r\n\r\n Please use CTRL-C in this window to terminate iPython Notebook on incline01\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 IPython Notebook in a Web Browser on nyx3<\/h3>\n
    On the nyx3<\/em> virtual desktop:<\/p>\n
      \n
    1. Start Iceweasel (e.g., using menu: Applications -> Internet -> Iceweasel<\/em>)<\/li>\n
    2. Now enter the following address in the browser address bar at the top:\n
      http:\/\/localhost:7777<\/pre>\n
      where 7777<\/code> is the number reported to you earlier when you ran ipython-notebook<\/code in the command window. Your number may be different!<\/li>\n<\/ol>\n
      You should now see the IPython Notebook dashboard<\/em> in your web browser. This has connected to the iCSF backend node running the IPython Notebook:<\/p>\n
      \n
    3. Iceweasel should already have the settings needed to access the outside world via the University proxy (this is done for security). If you cannot<\/em> access external websites, follow these instructions: <\/li>\n
        \n
      1. In Iceweasel, select the three hotdogs<\/em> menu on the right-hand side, then: Preferences<\/em><\/li>\n
      2. Select icon: Advanced<\/em> (cog icon in top row)<\/li>\n
      3. Select tab: Network<\/em> (middle of the 5 tabs)<\/li>\n
      4. Press button: Settings…<\/em> (top right of panel)<\/li>\n
      5. Select radio button: Manual proxy configuration:<\/em> (4th option)<\/li>\n
      6. Fill in the boxes HTTP Proxy: <\/em> webproxy.its.manchester.ac.uk<\/code> and Port: <\/em> 3128<\/code><\/li>\n
      7. Hit OK<\/li>\n
      8. Close the Preferences panel<\/li>\n<\/ol>\n<\/div>\n
        \"IPython<\/a><\/p>\n
        Create a new notebook in which you will run Python commands:<\/p>\n
          \n
        1. Press New Notebook<\/em> (right-hand side)<\/li>\n<\/ol>\n
          A new web browser tab will open giving you a notebook where you can type Python commands:<\/p>\n
          \"New<\/a><\/p>\n