Introductory Concepts to Computing

Natalie D. Tourville

January 20th, 2009

Atmospheric Science

Colorado State University

Summary of Topics

Operating system

Quick history of computing

Unix, Linux computing environments

Basic Unix commands

Shells – how to setup and use

Atmos Computing Environment

Getting help

Why care about the os?

Most critical software in a computer.

OS performance influences the performance of all software on a computerHow to extract the best performance out of an OS?How to work around design flaws? Write software

that takes advantage of the design of the OS

Why care about the os?

You need to understand enough to make informed decisions about things like: Buying and using a personal computer:Why do different PCs with the same CPU perform

differently?Should I get Windows XP? Windows 2000? Linux?

What’s the difference?Should I upgrade my hardware? Should I upgrade my

OS?What’s going on with my PC, especially when I have to

install something?Should I use disk compression? Is there a cost to using

it?

History of Computing

First generation 1945 - 1955 Technology: vacuum tubes & plugboards Programming: setting some switches Programming language: machine language Tasks: tables of sine, cosine, logarithms OS: none

Computer designer is: builder and programmer and operator and “sys admin”

History of Computers

Second generation 1955 – 1965 Technology: Transistors Programming: Punched cards Programming languages: FORTRAN & Assembly Tasks: Scientific Computer: Mainframes OS: Batch system

Universities started to buy computers (millions $)

Separation between computer designers, builders, operators, programmers and maintenance personnel.

– bring cards to IBM 1401 machine (good at card reading)– read cards to tape– put tape on IBM 7094 which does computing– put tape on IBM 1401 which prints output offline

History of Computing

• Third generation 1965 – 1980– Technology: Integrated circuits– Programming: Punched cards– Programming languages: FORTRAN & Assembly– Tasks: Scientific & commercial– Computers: IBM 360, DEC PDPs– OS: Multiprogramming/timesharing, spooling

• OSes Developed:– MULTICS (father of all modern OSes)– UNIX (System V, BSD)– POSIX – Portable Operating System Interface (by IEEE)– MINIX – 16 bit academic os (by Tanenbaum)– Linux (originated by Linus Torvalds, inspired by MINIX)

History of Computing

Fourth generation 1980-PresentProgramming: High level Programming languages: C/C++, Java, ……Computer: PC, rack mount systems, clustersOS: Windows, MacOS, Linux ……www.top500.org – 500 most powerful

computers

Cheap Desktop PCs

What is Linux?•Open source operating system

•Developed by Linus Torvalds at the U. of Helsinki in Finland since 1991.

•Under GNU GPL, its source code is free for everyone to download and use.

•One of the most popular, especially for a server markets

Linux

Source code can be modified to fit your need.

Quite portable – good for new hardware products

Supports various hardware platforms. Majority on x86

True multi-tasking operating system.

Being immunized against all kinds of viruses.

Linux

Linux supports many different types

Most commonly, ext2fs Filenames of 255 characters

File sizes up to 2GB+

File Systems 4TB+

Derived from extfs

Highly reliable and high performer

Many different flavors – Debian, RedHat, Ubuntu, Fedora, slackware, gentoo, etc.

Macintosh History

Mac OS X is a Unix-based operating system, built on technologies developed at NeXT between the second half of the 1980s and Apple's purchase of the company in early 1996

Mac OS X is based on the Mach kernel and is derived from the Berkeley Software Distribution (BSD)

named after large cats (leopard, tiger, etc)

Mac OS

Closed source with open source technology

Mac OS X's core is a POSIX compliant operating system (OS) built on top of the XNU kernel, with standard Unix facilities available from the command line interface.

Apple released this set of software as a free and open source operating system named Darwin.

On top of Darwin, Apple layered a number of components, including the Aqua interface and the Finder, to complete the GUI-based operating system which is Mac OS X.

Unix Basics

Access Control:“cd” “ls –l” and “chmod” commands rwx rwx rwx 7 7 7 rwx r_x r_x 7 5 5

Consulting the on-line manual man command

Compiling with “gcc” and “g++”

I/O Redirection

> Redirect output

< Redirect input

p & Run p in the background (try also jobs, ^Z, bg, fg, ps, and kill)

p1 | p2 Pipe output of p1 as input for p2

p >> f Append output of p into file f

Common operations

ls (list) command: directory’s contents (files and subdirectories)

• ls–l: in detail

• ls–a: hidden files also

• Wildcard: *: any string ?: any character

• Redirection: ls –l > somefile

• date: date and time

• whoami: current user

• finger a username: get someone’s login

Sample Unix commands

A subset of these commands are:

alias/unalias, bg, cat, cc, cd, chmod, cp, csh, diff, du echo, emacs, fg, gcc, grep, history, jobs, kill, ln, logout, lpq, lpr, lprm, ls, man, mkdir, more, mv, printenv, ps, pwd, rlogin, rm, rmdir, rsh, script, set, setenv, source tail, tar, telnet, touch, unset unsetenv uudecode, uuencode, vi, wc, which, xterm

Standard Files

UNIX concept of “standard files”

"standard input (where a command gets its input) -default is the terminal wc <input

"standard output (where a command writes it output) -default is the terminal ls -l >output

"standard error (where a command writes error messages) -default is the terminal

Create/edit a file

Vi, vim, gvim - http://bullium.com/support/vim.html

Emacs – http://refcards.com/docs/wingb/xemacs/xemacs-refcard-a4.pdf

Pico

joe

Any of you favorite editor

File Name ConventionsSome file names are special:

/ The root directory (don’t confuse with the root user)

. The current directory

.. The parent (previous) directory

~ My home directory

~jane - Jane’s home directory

Examples: ./a same as a

../jane/x go up one level then look in directory jane for x

pwd will tell where you are in the directory tree

Creating Files and Directories

Files can be created in a number of ways

The output of a command Being edited using vi or your favorite editor

By using the touch command which creates an empty file or updates the modification and access time information of an existing file

Directories are created using the mkdir command

Links

Links are references to files (aliases)

Two forms: HardSymbolicCan point to files on different physical devices Delete

of original leaves link / Delete of link leaves original Can be created for directoriesCreate using ln or ln -s command The ls –l command

will show you the links

File Permissions

Use the chmod command to change file and directory permissions

Important if you want to execute files/script or view web pages in your directory

The permissions are encoded as an octal number chmod 0755 file # Owner=rwx Group=r-x Other=r-x chmod 0500 file2 # Owner=r-x Group=--- Other=--- chmod 0644 file3 # Owner=rw- Group=r-- Other=r–

chmod +x file # Add execute permission to file for all chmod u-r file # Remove read permission for owner chmod a+w file # Add write permission for everyone

Getting around to other computers

ssh – secure protocol

telnet/ftp – insecure protocols

scp – secure copy transfer

ssh –Y – forward your X11 connections

mount

CSU VPN – recommended for accessing the CSU network from outside the network

Shells

sh - Bourne shell

the original csh - C shell -compatible with Bourne shell

bash - Bourne again shell -most common on Linux

tcsh - The enhanced C shell

zsh - Z shell -new, compatible with Bourne shell

ksh - Korn shell -most popular UNIX shell

Change your shell – chsh

Modify your shell - source

Bash shell - startupWhen Bash is invoked as an interactive login shell, or

as a non-interactive shell with the `--login' option, it first reads and executes commands from the file `/etc/profile', if that file exists.

After reading that file, it looks for `~/.bash_profile', `~/.bash_login', and `~/.profile', in that order, and reads and executes commands from the first one that exists and is readable. The `--noprofile' option may be used when the shell is started to inhibit this behavior.

When an interactive shell that is not a login shell is started, Bash reads and executes commands from `~/.bashrc’ (e.g. starting up a terminal).

Sample .bashrcThe ~/.bashrc file determines the behavior of the shell, and of shell

scripts. A proper understanding of this file can lead to more effective use of scripts.

#Setup: source this file in $HOME/.bashrc with following block$PATH=$PATH:/usr/bin:/usr/sbin:/bin:/sbin:.export PATH=$HOME/scripts:\$JAVA_HOME:/usr/share/java$JAVA_HOME/bin:/opt/javautil/bin:\# System shell commandsalias cp='cp -rvf’alias mv='mv -vf’alias ll='ls -l’alias la='ls -A’alias l='ls -CF’alias f='find . -name’alias s='sort’alias sdate='date +%d-%b-%Y’alias mdate='date +%d-%b-%Y_%H%M’alias ldate='date +%a_%d-%b-%Y_%H%M’alias psg='ps auxwww|grep -v grep | grep’alias hd='od -Ax -tx1z -v’alias printpath='readlink -f’alias tar='tar -vf’alias rsync='rsync -va’alias chmodx='chmod a+x’alias myip='nslookup `hostname`’alias reload='exec bash’# Application specfic commandsalias svnu='svn update’alias svnc='svn ci . -m’alias mb='mate $HOME/scripts/my.bashrc’alias ms='mate $HOME/scripts’#alias sshhub='ssh root@something.com'

Sample .cshrc file The .cshrc file in your home directory is read every time a new C-shell is

launched, and is used to ensure that the working environment is always correct. ----- Aliases ----- #

alias h history alias rm "rm i"

alias dir "ls -al | more" alias md mkdir alias rd rmdir

alias vt100 "set term=vt100" alias wy60 "set term=wyse60" # # ----- Environment Control ----- # mesg y # let other users write messages to my screen notify -y # inform me when mail arrives set history = 50 # remember the last 50 commands set path = ( /usr/bin /bin /usr/ucb/bin /usr/local/bin . ) #

Atmos Computing

Typically each group has own set of computers and or clusters for use to students.

Backbone network of 100 mbps to campus – gb backbone to annex, chemistry and acrc

Each group is different with a variety of platforms from Linux, Mac and Windows desktop

Atmos Computing

New computing facility located sw of the Annex

2000 sq ft with room for 84 racks

Tentatively scheduled for completion ~ January 2010

Current server room in middle of atmos build to accommodate 1970’s computing technology.

Modular components – AC and power

Getting Help

The Linux equivalent of HELP is man (manual)

"Use man -k <keyword> to find all commands with that keyword

"Use man <command>to display help for that command

#Output is presented a page at a time. Use b for to scroll backward, for a space to scroll forward and q to quit

Example – man ssh

Computing Help

System Administrator

internet/google for questions

Ask around – someone has already experienced the same problem you have

Questions?

Comments?