BI296: Linux and Shell Programming - cbb.sjtu.edu.cncbb.sjtu.edu.cn/course/bi296/lecture/lec01.pdf · BI296 Maoying Wu Outline CS-Fundamentals Linux Overview Operating System (OS)

BI296

Maoying Wu

Outline

CS-Fundamentals

Linux OverviewOperating System (OS)

Why Linux?

Linux vs. Windows vs.MacOS

Basic Knowledge

Linux Commands

BI296: Linux and Shell Programming

Maoying,[email protected]

Dept. of Bioinformatics & BiostatisticsShanghai Jiao Tong University

Spring, 2018

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Course OverviewI Course Description: Linux command line, system

administration and bash/python programmingI Prerequisite: NoneI Textbook: NoneI Grading: Grades will be determined roughly by

I Assignments: 20%I 5 Quizzes: 25% totalI 2 Take-home Practicals: 30%I Projects: 25%

I Exams: There will be 5 quizzes, 2 bring-homepracticals. All exams will be open-book, and willcover materials from lectures, discussions, labs andextracurricular readings.

I Webpage:http://cbb.sjtu.edu.cn/course/bi296

I Github:https://github.com/ricket-sjtu/bi028

http://cbb.sjtu.edu.cn/course/bi296

https://github.com/ricket-sjtu/bi028

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Course ScheduleSchedule is to be changed according to the practicalreasons.

I Lecture 01: Fundamental Knowledge about LinuxI Lecture 02: Dummy Linux CommandsI Lecture 03: Linux File System，Process

ManagementI Lecture 04: Regular Expression - GREP, SED and

AWKI Lecture 05: Shell Programming (BASH)I Lecture 06: System AdministrationI Lecture 07: Fundamental Python ProgrammingI Lecture 08: Data Structures and Algorithms in

PythonI Lecture 09: Scientific computing with PythonI Lecture 10: Python Data Science

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Assignment Policy

I To: [email protected] Title: lab1 516080910001I Attachment: lab1 5160809010001.tar.gzI Late Policy

I Solutions to assignments should be submitted beforethe due.

I Being late within 3 days will get the 50% grades.I Later more than 3 days will get no grades.

[email protected]

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Stop here and Ask

Any Questions?

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

fundamental concepts

I Central Processing Unit（CPU，中央处理器）I Graphical Processing Unit (GPU,图形处理器)I Cache（高速缓存）I Storage（存储）：bit, Byte, KB, MB, GB, TB, PB,

EB, ZBI Input/Output（输入输出）I Controller（控制器）

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Number system

I Decimal（十进制）I Binary（二进制）I Octal（八进制）I Hexadecimal（十六进制）

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Exercise

decimal binary octal hexadecimal12.68

10011107553

9FA5

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Machine digit（机器数的二进制表示）

I Original（原码）I One’s complement（反码）I Two’s complement（补码）

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Exercise

1. Convert these positive decimal to binary:I 133dI 25dI 73d

2. Convert these negative decimal values to negativebinary using one’s complement and two’scomplement(补码，假设计算机字长为8bit):

I -192dI -16dI -1dI -0d

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Network

I Host（主机）, Domain（域）I IP Adress, IPv4, IPv6I Physical Address (MAC Address)I Gateway(网关), netmask（子网掩码）I Domain Name Server（DNS，域名服务器）I Network Communication Protocol (网络通信协议)

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Next we will talk about ...

Course Outline

Fundamental Computer Science

Introduction to LinuxOperating System (OS)Why Linux?Linux vs. Windows vs. MacOSBasic KnowledgeLinux Commands

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

The Definition of Operating System (OS)WikipediaAn OS is a collection of software that manages computerresources (CPUs, memory, storage, etc.) and providesuniversal services for a set of computer programs.

Figure : Operating System

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

The principal tasks of OS

I Processor (CPU) Management（处理器管理）I Memory (Storage) Management（内存/存储管理）I Devices Management（其他设备管理）I Application Management（应用程序管理）I User Interface (UI)（提供用户接口）

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands


Course Outline



BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

What is Linux?

A free and open-source UNIX-like operating systemdeveloped under the GNU General Public License (GPL).

I Free and open source（自由、开源）.I More and more popular（时髦）, especially in the

field of scientific computing.I Portable（可移植）: Supports most of the available

computers

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

A Short History of UNIX

I Prototype: Multics by AT&T Bell Lab, GE and MITI 1969, UNIX by Ken Thompson and Dennis RitchieI 1973 UNIX rewritten with C (providing portability)I Berkeley UNIX (BSD UNIX)I 1983, System VI Commercial Products: SunOS, Solaris, HP-UX, AIX,

SCO-UNIX

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Advantages of UNIX

I Unix is very simpleI Implements only hundreds of system calls（系统调用）and

I have a straightforward, even basic design.I In UNIX, everything is a file, which unifies the

manipulation of data and devices into a set of coresystem calls.

I Kernels（内核）and all related system utilities arewritten in C and ASM

I Fast process creation and unique fork() system call.I Providing simple yet robust IPC（进程通信）primitives.

I Exhibiting clean layering, with a strong separationbetween policy (what to do) and mechanism (how todo).

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

A Short History of Linux (1)

I 1984, Richard Stallman, GNU ProjectI GNU’s Not Unix:http://www.gnu.orgI Copyleft

I Purpose: Free UNIXI Free as free speech, not free lunch.

I 1st step: re-implementation of UNIX utilities,especially

I C Compiler, C libraryI emacs/bash

I Free Software Foundation (FSF)I http://www.fsf.org

http://www.gnu.org

http://www.fsf.org

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

A Short History of Linux (2)

I 1991, Linus Torvalds, 1st version of Linux KernelI Initially on the 386 protected modeI Linus’s UNIX-Like OS = Linux

I 1992: 1st distributions emergedI Linux KernelI GNU and other toolsI Installation procedure

I The rest is well-known story ...I RedHat, Ubuntu, Debian, OpenSuSe, etc.

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

A Typical Computer System Architecture

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Programmer’s Viewpoint

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands


Course Outline



BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Linux, Windows, MacOS

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands


Course Outline



BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

M2: Multi-User and Multi-tasking

I Linux is a multi-user, multi-tasking OSI Multiple users can run multiple tasks simultaneously,

independent of each other.I Always need to “log in” before using the system

I Identify yourself with username + passwordI Ways to log in to the system

I Console: Directly attached keyboard, mouse, monitorI Serial terminalI Network connection (ssh, telnet, etc.)

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands


Course Outline



BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Linux Commands

I Many things on a Linux system can be done bytyping commands

I Note that the GUI (X-window) is not needed forrunning a Linux system.

I In order to type commands in X-window you need tostart a terminal emulator

I Command PromptI Can be configure yourself, the default isI $ - “logged in as a regular user”I # - “logged in as root (privileged user)”

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Start Linux

Now start Linux and log in as administrator“root”; and then open a terminal on yourdesktop. See, what’s your commandprompt?

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Command Syntax

Syntax format<command> [option(s)] [argument(s)]

Examples

# list files and directories in currentdirectory

ls# list files and directories lengthilyls -l# list files and directories in /devls /devls -al /dev

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Some Useful Commands

I passwd: Change your passwordI mkpasswd: Generate a random passwordI date, cal: Find out today’s date and display a

calendarI who, finger: Find out who else is active on the

systemI clear: Clear the screenI echo: Write a message to your screenI write, wall, talk, mesg: Inter-user

communicationI ...

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

who, what, where, where to go

I pwd: Print Working DirectoryI uname: Print the system informationI whoami: Who am II cd: Change working Directory

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

pwd: knowing where you are now

I Synopsis: pwdI All the path names are started with a slash (“/”), for

exampleI “/root” is the home directory for rootI “/home/xxx” is the home directory for user “xxx”I Use command “which pwd” can show you where

your command locatesI Most of the user commands are stored in /bin or

/usr/binI Commands for super user are in the directories /sbin

and /usr/sbin

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

uname: knowing what my system is

I Synopsis: uname option(s)

I uname -a: --all

I uname -i: --hardware-platform

I uname -m: --machine

I uname -n: --node-name

I uname -o: --operation-system

I uname -r: --kernel-release

I uname -s: --kernel-name

I uname -v: --kernel-version

I uname -p: --processor

I You can use uname --help to obtain moreinformation for this command.

I This command is very useful in compiling thesystem-dependent code.

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

whoami: knowing who you are

I Synopsis: whoamiI The command is different from “who am i”I and also “who”I Now guess what the command “who” can do for you?

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

cd: change directory to

I Synopsis: cd dir name

I Command “cd” without any argument will direct youto your home directory

I Command “cd ∼xxx” can direct you to the homedirectory of user “xxx”

I You can use either absolute pathname to visit thedirectory, e.g. “cd /tmp” or

I You can also use relative pathname to visit therelevant directory.

I If you are root, you can visit anywhere; but if you area normal user, maybe you will be forbidden to visitsomewhere, for example “/root”.

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

How to get help for a command

I “man” commandI for example “man ls” can return the manual for the

command “ls”I manpage is stored in the directory/usr/share/man/

I “info”I command --help or command -h

I HOWTO DocumentationI Refer to Internet

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

The man command (1)

I With the man command you can get the manualpage of commands

I Manual pages are stored in /usr/man or/usr/share/man

I The manual page consists of:I NAME: The name of the command and a online

descriptionI SYNOPSIS: The syntax of the commandI DESCRIPTION: Explanation of how the command

works and what it doesI Files: The files used by the commandI Bugs: Known bugs and errorsI See Also: Other relevant commands

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

The man command (2)

I The “-k” optionI man -k print

I Manual pages are divided into 8 sections:1. User commands2. System calls3. Libc calls4. Devices5. File formats and protocols6. Games7. Conventions, macro packages and so forth8. System administration

I To select the correct section, add section number:I man 1 passwdI man 5 passwd

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Working with Files and Directories

What is a file?I A collection of dataI An object that can be read from, or written to, or both.I All the objects in Linux are filesI A file has certain attributes include

I File typeI Access permissions

File StructureI Generally: byte stream, record sequence, record treeI In Linux: byte stream

BI296

Maoying Wu

Outline

CS-Fundamentals


Why Linux?


Basic Knowledge

Linux Commands

Directory Structure

I Linux File System Standard:http://www.pathname/fhs

http://www.pathname/fhs

Documents

BI296: Linux and Shell Programming - cbb.sjtu.edu.cncbb.sjtu.edu.cn/course/bi296/lecture/lec01.pdf · BI296 Maoying Wu Outline CS-Fundamentals Linux Overview Operating System (OS)