Using the Command line Interface

Short introduction to the command line interface (CLI)

The CLI provides a direct way to interact with the Operating System, by typing in commands.

Why the CLI is worth learning

  • Might be the only interface you have to a High Performance Computer (HPC)
  • Command statements can be reused easily and saved as scripts
  • Easier automation and text files manipulation

A little bit of terminology

  • Command Line Interface (CLI): This is a user interface that lets you interact with a computer. It is a legacy from the early days of computers. Now a days computers have graphical user interfaces instead (MacOSX, Windows, Linux, …)
  • Terminal: It is a an application that lets you run a command line interface. It used to be a physical machine connected to a mainframe computer
  • Shell: It is the program that runs the command line. There are many different shells, the most common (an default on most system) being bash (Bourne Again SHell)
Tip

Not convinced? Check this out: the CLI pitch

The Terminal from RStudio

You can access the command line directly from RStudio by using the Terminal tab next to your R console.

Permissions

All files have permissions and ownership.

File permissions
  • List files showing ownership and permissions: ls -l
brun@taylor:/courses/EDS214$ ls -l
total 16
drwxrwxr-x+ 3 brun      esmdomainusers 4096 Aug 20 04:49 data
drwxrwxr-x+ 2 katherine esmdomainusers 4096 Aug 18 18:32 example

You can change those permissions:

  • Change permissions: chmod
  • Change ownership: chown
Tip

Clear contents in terminal window: clear

General command syntax

  • command [options] [arguments]

where command must be an executable file on your PATH * echo $PATH

and options can usually take two forms * short form: -a * long form: --all

You can combine the options:

ls -ltrh

What do these options do?

man ls
Tip

hit spacebar to get to the next page of the manual hit q to exit the help

Connecting to a remote server via ssh

From the gitbash (MS Windows) or the terminal (Mac) type:

ssh taylor.bren.ucsb.edu

You will be prompted for your username and password.

aurora_ssh

You can also directly add your username:

ssh brun@taylor.bren.ucsb.edu

In this case, you will be only asked for your password as you already specified which user you want to connect with.

Unix systems are multi-user

  • Who else is logged into this machine? who
  • Who is logged into “this shell”? whoami

Getting help

  • <command> -h, <command> --help
  • man, info, apropos, whereis
  • Search the web!

finding stuff

Show me my Rmarkdown files!

find . -iname '*.Rmd'

Which files are larger than 1GB?

find . -size +1G

With more details about the files:

find . -size +1G -ls

Getting things done

Some useful, special commands using the Control key

  • Cancel (abort) a command: Ctrl-c Note: very different than Windows!!
  • Stop (suspend) a command: Ctrl-z
  • Ctrl-z can be used to suspend, then background a process

Process management

  • Like Windows Task Manager, OSX Activity Monitor
  • top, ps, jobs (hit q to get out!)
  • kill to delete an unwanted job or process
  • Foreground and background: &

What about “space”

  • How much storage is available on this system? df -h
  • How much storage am “I” using overall? du -hs <folder>
  • How much storage am “I” using, by sub directory? du -h <folder>

History

  • See your command history: history
  • Re-run last command: !! (pronounced “bang-bang”)
  • Re-run 32th command: !32
  • Re-run 5th from last command: !-5
  • Re-run last command that started with ‘c’: !c

A sampling of simple commands for dealing with files

  • wc count lines, words, and/or characters
  • diff compare two files for differences
  • sort sort lines in a file
  • uniq report or filter out repeated lines in a file

Get into the flow, with pipes

stdin, stdout, stderr
$ ls *.png | wc -l
$ ls *.png | wc -l > pngcount.txt
$ diff <(sort file1.txt) <(sort file2.txt)
$ ls foo 2>/dev/null
  • note use of * as character wildcard for zero or more matches (same in Mac and Windows)
  • ? matches single character; _ is SQL query equivalent

Text editing

Some editors

  • vim
  • emacs
  • nano
$ nano .bashrc

Hands-on

Let’s practice our new skills! Click here

Aknowledgements

This section adapted materials from NCEAS Open Science for Synthesis (OSS) intensive summer schools and other training. Contributions to this content have been made by Mark Schildhauer, Matt Jones, Jim Regetz and many others; and from EDS-213 10 bash essentials developed by Greg Janée

This work is licensed under CC BY 4.0

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