2018年2月22日 星期四

[Linux 文章收集] How To Set Up a Jupyter Notebook to Run IPython on Ubuntu 16.04

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Introduction 
IPython is an interactive command-line interface to Python. Jupyter Notebook offers an interactive web interface to many languages, including IPython. 

This article will walk you through setting up a server to run Jupyter Notebook as well as teach you how to connect to and use the notebook. Jupyter notebooks (or simply notebooks) are documents produced by the Jupyter Notebook app which contain both computer code (e.g. Python) and rich text elements (paragraph, equations, figures, links, etc.) which aid in presenting reproducible research. 

By the end of this guide, you will be able to run Python 2.7 code using Ipython and Jupyter Notebook running on a remote server. For the purposes of this tutorial, Python 2 (2.7.x) is used since many of the data science, scientific computing, and high-performance computing libraries support 2.7 and not 3.0+. 

Prerequisites 
To follow this tutorial, you will need the following: 
* Ubuntu 16.04 Droplet
* Non-root user with sudo privileges (Initial Server Setup with Ubuntu 16.04 explains how to set this up.)

All the commands in this tutorial should be run as a non-root user. If root access is required for the command, it will be preceded by sudo. Initial Server Setup with Ubuntu 16.04 explains how to add users and give them sudo access. 

Step 1 — Installing Python 2.7 and Pip 
In this section we will install Python 2.7 and Pip. 

First, update the system's package index. This will ensure that old or outdated packages do not interfere with the installation. 
$ sudo apt-get update

Next, install Python 2.7, Python Pip, and Python Development
$ sudo apt-get -y install python2.7 python-pip python-dev
$ pip install --upgrade pip
$ python --version
Python 2.7.12
$ pip --version
pip 9.0.1 from /usr/local/lib/python2.7/dist-packages (python 2.7)

Installing python2.7 will update to the latest version of Python 2.7, and python-pip will install Pip which allows us to manage Python packages we would like to use. Some of Jupyter’s dependencies may require compilation, in which case you would need the ability to compile Python C-extensions, so we are installing python-dev as well. 

Step 2 — Installing Ipython and Jupyter Notebook 
In this section we will install Ipython and Jupyter Notebook. 

First, install Ipython: 
$ sudo apt-get -y install ipython ipython-notebook
$ ipython --version
5.5.0

Now we can move on to installing Jupyter Notebook: 
// -H, --set-home
// Request that the security policy set the HOME environment variable to the home directory specified by the target user's password database entry.

$ sudo -H pip install jupyter
$ python -c "import jupyter; print jupyter.__version__"
1.0.0
$ pip list | grep 'jupyter'
jupyter (1.0.0)
jupyter-client (5.2.2)
jupyter-console (5.2.0)
jupyter-core (4.4.0)

Step 3 — Running Jupyter Notebook 
You now have everything you need to run Jupyter Notebook! To run it, execute the following command: 
$ jupyter notebook

If you are running Jupyter on a system with JavaScript installed, it will still run, but it might give you an error stating that the Jupyter Notebook requires JavaScript: 
Jupyter Notebook requires JavaScript.
Please enable it to proceed.
...

To ignore the error, you can press Q and then press Y to confirm. 

A log of the activities of the Jupyter Notebook will be printed to the terminal. When you run Jupyter Notebook, it runs on a specific port number. The first notebook you are running will usually run on port 8888. To check the specific port number Jupyter Notebook is running on, refer to the output of the command used to start it: 
[I NotebookApp] Serving notebooks from local directory: /home/sammy
[I NotebookApp] 0 active kernels
[I NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
...

If you are running Jupyter Notebook on a local Linux computer (not on a Droplet), you can simply navigate to localhost:8888 to connect to Jupyter Notebook. If you are running Jupyter Notebook on a Droplet, you will need to connect to the server using SSH tunneling as outlined in the next section. 

At this point, you can keep the SSH connection open and keep Jupyter Notebook running or can exit the app and re-run it once you set up SSH tunneling. Let's keep it simple and stop the Jupyter Notebook process. We will run it again once we have SSH tunneling working. To stop the Jupyter Notebook process, press CTRL+C, type Y, and hit ENTER to confirm. 

Step 4 — Connecting to the Server Using SSH Tunneling 
In this section we will learn how to connect to the Jupyter Notebook web interface using SSH tunneling. Since Jupyter Notebook is running on a specific port on the Droplet (such as :8888, :8889 etc.), SSH tunneling enables you to connect to the Droplet's port securely. The next two subsections describe how to create an SSH tunnel from 1) a Mac or Linux and 2) Windows. Please refer to the subsection for your local computer. 

SSH Tunneling with a Mac or Linux 
If you are using a Mac or Linux, the steps for creating an SSH tunnel are similar to the How To Use SSH Keys with DigitalOcean Droplets using Linux or Mac guide except there are additional parameters added in the ssh command. This subsection will outline the additional parameters needed in the ssh command to tunnel successfully. 

SSH tunneling can be done by running the following SSH command: 
# ssh -L 0.0.0.0:1234:localhost:8888 @ // Replace and as your need
# netstat -tunlp | grep 1234
tcp 0 0 0.0.0.0:1234 0.0.0.0:* LISTEN 65554/ssh

The ssh command opens an SSH connection, but -L specifies that the given port on the local (client) host is to be forwarded to the given host and port on the remote side (Droplet). This means that whatever is running on the second port number (i.e. 8888) on the Droplet will appear on the first port number (i.e. 8000) on your local computer. You should change 8888 to the port which Jupyter Notebook is running on. Optionally change port 8000 to one of your choosing (for example, if 8000 is used by another process). Use a port greater or equal to 8000 (ie 8001, 8002, etc.) to avoid using a port already in use by another process. is your username (i.e. sammy) on the Droplet which you created and is the IP address of your Droplet. For example, for the username sammy and the server address 111.111.111.111, the command would be: 
# ssh -L 8000:localhost:8888 sammy@111.111.111.111

If no error shows up after running the ssh -L command, you can run Jupyter Notebook: 
# jupyter notebook

Now, from a web browser on your local machine, open the Jupyter Notebook web interface with http://localhost:8000 (or whatever port number you chose). 

Step 5 — Using Jupyter Notebook 
This section goes over the basics of using Jupyter Notebook. By this point you should have Jupyter Notebook running, and you should be connected to it using a web browser. Jupyter Notebook is very powerful and has many features. This section will outline a few of the basic features to get you started using the notebook. Automatically, Jupyter Notebook will show all of the files and folders in the directory it is run from. 

To create a new notebook file, select New > Python 2 from the top right pull-down menu: 
 

This will open a notebook. We can now run Python code in the cell or change the cell to markdown. For example, change the first cell to accept Markdown by clicking Cell > Cell Type > Markdown from the top navigation bar. We can now write notes using Markdown and even include equations written in LaTeX by putting them between the $$ symbols. For example, type the following into the cell after changing it to markdown: 
  1. # Simple Equation  
  2.   
  3. Let us now implement the following equation:  
  4. $$ y = x^2$$  
  5.   
  6. where $x = 2$  
To turn the markdown into rich text, press CTRL+ENTER, and the following should be the results: 
 

You can use the markdown cells to make notes and document your code. Let's implement that simple equation and print the result. Select Insert > Insert Cell Below to insert and cell and enter the following code: 
  1. x = 2  
  2. y = x*x  
  3. print y  
To run the code, press CTRL+ENTER. The following should be the results: 
 

You now have the ability to include libraries and use the notebook as you would with any other Python development environment! 

Conclusion 
Congratulations! You should be now able to write reproducible Python code and notes using markdown using Jupyter notebook running on a Droplet. To get a quick tour of Jupyter notebook, select Help > User Interface Tour from the top navigation menu. 

Supplement 
How To Set Up SSH Tunneling on a VPS

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