Python programming¶

This page describes how to program in Python on the UPPMAX clusters.

There are multiple ways to program in Python:

Description	Features
Use a text editor	Non-interactive, no help
Use the Python interpreter	Interactive, terminal-based, some help
Use IPython	Interactive, terminal-based, more help and features
Use Jupyter	Interactive, web-based
Use Visual Studio Code	Interactive, install on local computer, use locally installed Python and Python packages

How does a text editor look like?

GNU nano

A text editor, in this case, GNU nano

How does a Python interpreter look like?

A Python interpreter

A Python interpreter

How does IPython look like?

IPython

IPython

Use a text editor¶

Using a text editor to program in Python is a simple way to write code: it is the same as writing any text file.

Here we use the text editor GNU nano to write a Python script:

nano example_script.py

Within nano, write:

print('Hello, world!')

To save, press CTRL + O (i.e. the letter), then enter to keep the same filename
To quite, press CTRL + Q

You can run this Python script in the shell by:

python example_script.py

or, if you want to be explicitly use Python 3:

python3 example_script.py

Some features of this approach are:

this is a simple way to write code: it is the same as writing any text file.
you get no help while writing code
you can only run the script from start to finish, i.e. you cannot partially run the script

How to run a Python script line-by-line?

You can run a Python script line-by-line using a Python debugger, such as pdb.

On the terminal, for python, do:

pdb example_script.py

or for python3:

pdb3 example_script.py

See the official Python documentation of pdb here.

Use the Python interpreter¶

After loading a Python module, you have the Python interpreter available.

Forgot how to load a Python module?

See the UPPMAX page about Python here.

What is a Python interpreter?

In computing, an interpreter is a program that reads text and runs it directly, without any additional steps.

The Python interpreter runs the Python commands you type directly, without any additional steps.

Start the Python interpreter by typing:

python

or (for explicit Python 3):

python3

The Python prompt looks like this:

>>>

Type, for example:

print('Hello, world!')

and the interpreter will run the statement.

Exit the Python interpreter with <Ctrl-D>, quit() or exit().

The Python interpreter gives limited auto-complete while writing code

How do I get auto-complete?

As an example, writing this line of code in the Python interpreter ...

s = 'Hello, world!'

... and press enter. Now a variable called s will hold some text.

Now type ...

s.

and press Tab twice. You will see a list of things you can do with that string.

The Python interpreter can show graphics.

How do I get the Python interpreter to show graphics?

In the Python interpreter, run this code line-by-line:

import matplotlib.pyplot as plt
plt.plot([1, 4, 9, 16])
plt.show()

(or as a one-liner: import matplotlib.pyplot as plt; plt.plot([1, 4, 9, 16]); plt.show())

You will see a window appear:

You will only see a window appear, if you've logged in to Rackham with SSH with X forwarding enabled.

Spoiler: ssh -X sven@rackham.uppmax.uu.se.

The Python interpreter cannot directly run scripts.

Use IPython¶

IPython is a console program that extends the regular Python interpreter: among others, one can directly run scripts and re-use output.

Want to see a video?

Here are some videos on IPython:

After loading a Python module, you also have the IPython Python command shell available.

Forgot how to load a Python module?

See the UPPMAX page about Python here.

What is a Python command shell?

In computing, a shell is a a program around something, for example, Bash is a shell around a UNIX-like operating system.

In computing, a command shell means that the shell is a command-line shell, i.e. text only.

A Python command shell, hence, is a text-only program around Python.

Start the IPython command shell by typing:

ipython

or (for explicit Python 3):

ipython3

The ipython3 prompt looks like this:

[richel@rackham1 ~]$ ipython
Python 3.11.4 (main, Aug  7 2023, 16:05:58) [GCC 12.2.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.14.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]:

IPython allows one to write code interactively.

For example, in IPython, type:

print('Hello, world!')

and IPython will show the result of that line of code.

IPython can interact with your file system.

How does IPython interact with the file system?

For example, within IPython, running ...

```python ls ````

... displays a list of files in your current working folder in the same way as Bash's ls.

The Python interpreter will give an error if you do the same.

IPython has an auto-complete triggered by Tab.

How do I get auto-complete?

As an example, writing this line of code in IPython ...

s = 'Hello, world!'

... and press enter. Now a variable called s will hold some text.

Now type ...

s.

and press Tab. You will see a menu of things you can do with that string. Hold tab to scroll through the many options.

IPython can show graphics.

How do I get IPython to show graphics?

In IPython, run this code line-by-line:

import matplotlib.pyplot as plt
plt.plot([1, 2, 3, 4])
plt.show()

(or as a one-liner: import matplotlib.pyplot as plt; plt.plot([1, 2, 3, 4]); plt.show())

You will see a window appear:

You will only see a window appear, if you've logged in to Rackham with SSH with X forwarding enabled.

Spoiler to login: ssh -X sven@rackham.uppmax.uu.se.

Spoiler to confirm: xeyes

IPython can directly run scripts.

How do I get IPython to directly run scripts?

In IPython, run:

run [filename]

where [filename] is the name of a file, for example:

run my_script.py

IPython will run the script and remember variables, functions and classes created in that script.

Use Jupyter¶

Some features are:

interactive
web-based

Use Visual Studio Code¶