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IMSE 8410 Command Line Interface

IMSE 8410 Advanced Computational Systems and Data Engineering

Material Copyright 2017-2019 by Timothy Middelkoop. Source code licensed under the Apache License, Version 2.0. Documentation licensed under CC by SA 3.0.

Command Line Interface (CLI)

"Vísteme despacio que estoy de prisa" ("Dress me slowly, for I'm in a hurry") - Napoleon Bonaparte

Objectives

In this module we will cover the fundamentals of the CLI in a Linux environment. We leave the specifics of the commands to the reading and to the man pages.

By the end of this module students should be:

  • Familiar with basics of the Command Line Interface in order to execute commands on a High Performance Computing (HPC) cluster.
  • Familiar with the basics of the BASH shell, specifically with the following concepts that also apply more broadly:
    • Paths (relative, absolute, pwd)
    • Commands, options, and arguments
    • Environment variables (${PATH}, ${USER}, ${HOME})
    • Users, groups, and permissions
    • Processes
    • File globbing
    • Command line expansion
    • Escaping escaping
    • Looping and logic
    • Redirection; stdin, stdout, stderr
    • Editing files
    • Scripting and the Shebang

Background

The Command Line Interface, often called the CLI, can be daunting and frustratingly spartan at first but over time becomes a fast, natural, and very powerful interface.

Early systems were connected to a typewriter for input and a line printer for output [HW: verification and citation needed]. Today this has changed very little and when it comes to most interactions remains the same. The only real change is the adoption of monitors and the adoption of Unicode using UTF-8 over ASCII (which is backwards compatible).

command

and

response

The spirit of the "Unix philosophy" is "Do One Thing and Do It Well," and such Unix and Linux is just a collection of small commands that, when put together, make the whole. In this module we will be discussing the general framework, not the specifics of the tools, and how it is all put together.

Compute

This framework requires different programs (the process) to run and interact in a multi-user environment in order to accomplish some useful work.

The process is the fundamental unit of "compute."

"In the beginning there was init"

The init process (magically, and now using systemd) is responsible for running all the programs to setup and run the system.

A program is launched, runs, and then terminates. Each process has a number (called a pid) and has a parent process and a number of child process.

Configuration

Processes can get configuration information through environment variables. Environment variables are KEY=value pairs and each process has it's own (mutable) environment. Child process get their own copy of the environment, allowing for the parent to pass configuration information to the child.

Storage

The file is the fundamental unit of storage. A file has a name, ownership, permissions, and a location. In Linux files live in directories and directories are arranged into a single hierarchy of files starting with the root (/) folder. Processes can access files either by specifying a absolute path starting with / or a relative path. The relative path is a folder that starts with the processes present working directory or PWD. Each process has a PWD (that can change) and children inherent the parents PWD.

There are two special folders named . and .., which represent the current and parent directories, relative to the folder that they are in.

Networking

In Linux communication between processes is accomplished though pipes - the network. These pipes can be either local or over the network. In the CLI this is most often the stdin, stdout, and stderr. Process pass information from their stdout to a child's stdout (we will convently ignore stderr) though the use of redirection. This information is in the form of a stream of bytes that is buffered between each process, and each process can run simultaneously.*. Redirection also allows directing streams to and from files (hence the name). In this way a number of commands can be chained together transforming the information along the way.

Basic Linux

There are a number of good tutorials and videos online. We use the HPC Carpentry website section on the Linux Shell (https://hpc-carpentry.github.io/hpc-shell/) sections 1-4.

To get help run the man command with the first argument with the name of the command. Many programs you can also just run the command with --help, for example man --help.

CLI Concepts:

  • prompt/shell, path, file, program, arguments, switches

Basic commands:

  • man, ls, pwd, cd, mkdir, rmdir, mv, rm, echo, touch, cat, less, grep, wc, sort, gzip
  • git
  • ssh, wget, curl, rsync
  • tar, unzip, zip
  • exit

Redirection:

  • <, >, >>, |,

Editors:

  • nano, emacs, vi

Examples

See the Module 4 notebooks in Jupyter for examples.

Reading