Why Use the Command Line?

We will interact with the operating system via a command-line interface. We are all used to the point-and-click graphical user interfaces of modern computers. So why use the command line?

There are a few reasons (and see the excellent discussion that is part of the Software Carpentry Unix shell notes):

• Scientific computing often involves automating workflows and repetitive tasks.

  We want to eliminate the potential for a person to make mistakes as much as possible, to ensure reproducibility. Writing scripts for our workflows promotes this.

• Supercomputing facilities are access via remote connections and almost exclusively use some type of Linux OS.

  Tip

  Take a look at the Top 500 list of fastest computers

  Even a research group’s server is likely accessed remotely.

• Much of the analysis software we use is written as a command line tool that is meant to be incorporated into a script, or chained together with other tools.

• It helps us understand how the computer thinks about our files and data.

• Unix/Linux is a multi-user operating system. We often will be using shared-resources in a research group. This means we will not be sitting directly in front of the computer.

The MathLab machines run Linux which is an open-source Unix-like operating system. Linux powers much of the internet and high-performance computing systems.

Note

You may already be using a Unix-like operating system.

• ChromeOS / chromebooks are running Linux

• Android phones are running Linux

• MacOS is a Unix-like operating system (it just hides it by default)

• many embedded systems run Linux (routers, TVs, car entertainment systems, …)