University:
Boston University
Course:
MET CS 201 | Introduction to Programming
Academic year:

2023
Views:

98

Pages:

64
Author:

repasataby7g

Introduction to Linux Topics for Today ● ● ● ● ● ● ● ● Research Computing Services Linux Overview Linux Interaction - Shell and Commands I/O redirection (pipes, etc.) Navigating the file system Processes and job control Editors Creating and Running Code Research Computing Services Research Computing Services (RCS) A group within Information Services & Technology at Boston University provides computing, storage, and visualization resources and services to support research that has specialized or highly intensive computation, storage, bandwidth, or graphics requirements. Three Primary Services: ● Research Computation ● Research Visualization ● Research Consulting and Training RCS Team and Expertise Our Team Consulting Focus: ● ● ● ● ● ● ● ● ● ● ● Scientific Programmers Systems Administrators Service Management Specialists Research Facilitators Special Initiatives (Grants) Bioinformatics Data Analysis / Statistics Molecular modeling Geographic Information Systems Scientific/Engineering Simulation Visualization You ● Who has experience programming? ● Using Linux? ● Using compute clusters? ● Using the Shared Computing Cluster (SCC)? Linux What, Who, When, Where & Why What is Linux ● Unix-like computer operating system assembled under the model of free and open-source software development and distribution. ● These operating systems share the Linux kernel. ○ ● Typically have the GNU utilities Comes in several “distributions” to serve different purposes. What is Linux gcc wc ● Bird’s eye view emacs bash multitasking device access cat Hardware file system tcsh grep sh sort Kernel Shell Utilities awk Who is Linux & ● Linux is an O/S core originally written by Linus Torvalds. Now almost 10,000 developers including major technology companies like Intel and IBM. ● A set of programs written by Richard Stallman and others. They are the GNU utilities. When is Linux? ~1991 Where is Linux ● World Wide Web ○ 67% of the world’s web-servers run Linux (2016) ● Research/High-Performance Compute ○ Google, Amazon, NSA, 100% of TOP500 Super-computers. ● Modern Smartphones and devices ○ The Android phone ○ Amazon Kindle ○ Smart TVs/Devices Why Linux ● Free and open-source. ● Powerful for research datacenters ● Personal for desktops and phones ● Universal ● Community (and business) driven. Connecting Let’s use Linux Local System Remote Server Connection Protocols and Software Remote Connections: Remote Graphics: Data Transfer: Secure SHell (SSH) X-Windowing (X, X-Win) Secure File Transfer Protocol (SFTP) Other protocols too, but let’s start with these. Connecting from Different Platforms SSH Microsoft Windows X-Win SFTP MobaXterm https://mobaxterm.mobatek.net Apple macOS Terminal (Built in) XQuartz https://www.xquartz.org Cyberduck https://cyberduck.io Linux Terminal (Built in) X11 (Built in) Various (Built in) Microsoft Windows You need software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ● Recommended: MobaXterm ○ Download: http://mobaxterm.mobatek.net/ ● Alternatives: ○ SSH/X-Windows: X-Win32 https://www.bu.edu/tech/services/support/desktop/distribution/xwindows/ ○ SFTP: Filezilla https://filezilla-project.org/ Apple macOS ● SSH: Terminal Built in! Apple macOS is built on Darwin -- a derivative of 4.4BSD-Lite2 and FreeBSD ○ Built in to macOS Applications > Utilities > Terminal ● X-Windows: XQuartz ○ Download: https://www.xquartz.org/ ○ Note: This install requires a logout. ● SFTP: Your choice ○ Filezilla: https://filezilla-project.org/ ○ Cyberduck: https://cyberduck.io ○ Many others (Cross-platform, open-source) (macOS native, drag-and-drop) Linux ● SSH: Terminal ○ Built in to Linux Applications > System > Terminal ● X-Windows: X11 ○ Built in to Linux ○ Use your package manager. ● SFTP: Your choice ○ Usually has one Built in. ○ Alternate: Filezilla (https://filezilla-project.org/) Connecting ● Use your Shared Computing Cluster account if you have one. ● Tutorial accounts if you need one. ○ Username: Tutorial credentials blocked for print. ○ Password: This box disappears during presentation [local_prompt]$ ssh username@scc1.bu.edu username@scc1.bu.edu’s Password: [username@scc1 ~]$ Get supplementary files ● At the command prompt, type the following: [username@scc1 ~]$ cd ~ [username@scc1 ~]$ tar xf /scratch/linux-materials.tar [username@scc1 ~]$ ls c data haystack scripts Linux Interaction Shell, Prompt, Commands and System Use Linux: The Shell ● Program that interprets commands and sends them to the OS ● Provides: ○ Built-in commands ○ Programming control structures ○ Environment variables ● Linux supports multiple shells. ○ The default on SCC is Bash. “Bash” = “Bourne-again Shell” (GNU version of ~1977 shell written by Stephen Bourne) Linux: The “prompt” Your Username Current Directory [username@scc1 ~]$ The System Name Input ( In Linux “ ~ ” is a shorthand for your home directory. ) Linux: Command Basics [username@scc1 ~]$ command --option argument ● Command: Command/program that does one thing ● Options: Change the way a command does that one thing ○ Short form: ○ Long form: Single-dash and one letter Double-dash and a word e.g. e.g. ls -a ls --all ● Argument: Provides the input/output that the command interacts with. For more information about any command, use man or info (e.g. “man ls”) Commands: Hands-On ● After you connect, type ○ ○ ○ ○ ○ ○ ○ ○ whoami hostname echo “Hello, world” echo $HOME echo my login is $(whoami) date cal shazam # my login # name of this computer # print characters to screen # print environment variable # replace $(xx) with program output # print current time/date # print this month’s calendar # bad command Commands: Hands-On Options ● Commands have three parts; command, options and arguments/parameters. Example: cal –j 3 1999. “cal” is the command, “-j” is an option (or switch), “3” and “1999” are arguments/parameters. [username@scc1 ~]$ cal -j 3 1999 ● ● What is the nature of the prompt? What was the system’s response to the command? Commands “Small programs that do one thing well” ● The Unix Programming Environment, Kernighan and Pike … at its heart is the idea that the power of a system comes more from the relationships among programs than from the programs themselves. Many UNIX programs do quite trivial things in isolation, but, combined with other programs, become general and useful tools. Commands: Selected text processing utilities ● ● ● ● ● ● ● ● ● ● ● ● ● ● awk cat cut diff grep head less sed sort split tail tr uniq wc Pattern scanning and processing language Display file(s) Extract selected fields of each line of a file Compare two files Search text for a pattern Display the first part of files Display files on a page-by-page basis Stream editor (esp. search and replace) Sort text files Split files Display the last part of a file Translate/delete characters Filter out repeated lines in a file Line, word and character count Just a few of the commands for text processing Variables and Environment Variables ● Variables are named storage locations. ○ USER=augustin ○ foo=“this is foo’s value” ● “Environment variables” are variables used and shared by the shell ○ For example, $PATH tells the system where to find commands. ● Environment variables are shared with programs that the shell runs. Bash variables ● To create a new variable, use the assignment operator ‘=‘ [username@scc1 ~]$ foo=“this is foo’s value” ● The foo variable can be printed with echo [username@scc1 ~]$ echo $foo this is foo’s value ● To make $foo visible to programs run by the shell (i.e., make it an “environment variable”), use export: [username@scc1 ~]$ export foo Environment Variables ● To see all currently defined environment variable, use printenv: [username@scc1 ~]$ printenv HOSTNAME=scc1 TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 TMPDIR=/scratch SSH_CLIENT=168.122.9.131 37606 22 SSH_TTY=/dev/pts/191 USER=cjahnke MAIL=/var/spool/mail/cjahnke PATH=/usr3/bustaff/cjahnke/apps/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin PWD=/usr3/bustaff/cjahnke/linux-materials LANG=C MODULEPATH=/share/module/bioinformatics:/share/module/chemistry SGE_ROOT=/usr/local/ogs-ge2011.11.p1/sge_root HOME=/usr3/bustaff/cjahnke Command History and Command Line Editing ● Try the history command ● Choose from the command history using the up ↑ and down ↓ arrows ● To redo your last command, try !! ● To go further back in the command history try !, then the number as shown by history (e.g., !132). Or, !ls, for example, to match the most recent ‘ls’ command. ● What do the left ← and right → arrow do on the command line? ● Try the and keys Help with Commands ● Type ○ ○ ○ date –-help man date info date ● BASH built-ins ○ ○ ○ A little different from other commands Just type the command ‘help’ Or ‘man bash’ Yes, you can always Google it. On using ‘man’ with ‘less’ ● The man command outputs to a pager called less, which supports many ways of scrolling through text: ○ ○ ○ ○ ○ ○ ○ ○ Space, f b < > / ? h q # page forward # page backward # go to first line of file # go to last line of file # search forward (n to repeat) # search backward (N to repeat) # display help # quit help I/O Redirection I/O redirection with pipes ● Many Linux commands print to “standard output”, which defaults to the terminal screen. The ‘|’ (pipe) character can be used to divert or “redirect” output to another program or filter. ○ ○ ○ ○ ○ w w w w w | | | | less grep grep grep # show who’s logged on # pipe into the ‘less’ pager ‘tuta’ # pipe into grep, print lines containing ‘tuta’ –v ‘tuta’ # print only lines not containing ‘tuta’ ‘tuta’ | sed s/tuta/scholar/g # replace all ‘tuta’ with ‘scholar’ More examples of I/O redirection ● Try the following (use up arrow to avoid retyping each line): ○ w | wc ○ w | cut –d ‘ ’ –f1 | sort ○ w | cut –d ‘ ’ –f1 | sort | uniq # count lines # sort users # eliminate duplicates ● We can also redirect output into a file: ○ w | cut –d ‘ ’ –f1 | sort | uniq > users ● Note that ‘awk’ can be used instead of ‘cut’: ○ w | awk ‘{print $1;}’ | sort | uniq > users ● Quiz: ○ How might we count the number of distinct users currently logged in? For extra credit, how can we avoid over-counting by 2? (Hint: use ‘tail’.) The Filesystem The Linux File System ● ● ● ● The structure resembles an upside-down tree Directories (a.k.a. folders) are collections of files and other directories. Every directory has a parent except for the root directory. Many directories have subdirectories. / / ЕТС /BIN "ESSENTIAL BINARIES" САТ CHGRP CHUOD CHOWN СР DATA DD DF DUESG ЕСНО FALSE HOSTNAUE KILL LN LOGIII LS IIKDIR IIKHOD IIORE IIOUN T IIV PS PWD RM RUDIF SED sн SТТУ su SYNCH TRUE UMOU N T UNAIIE " НОSТ SPECFIC SYSTEII COHFIG" /ВООТ "STATIC FLE S OF ВООТ LOADER " KERNEL SYSТEU.UAP VULINUZ INIТRD GRUB UODULEJNFO воот CSH. LOGIN EXPORТS FSTAВ FТPUSERS GATEWAYS GEТТYDEFS GROUP HOST.CONF HOSТS HOSТS. ALLOW HOSТS.DENY HOSТS.EQUIV HOSТS.LPD IHE TD.CONF ,нmАв ISSUE LS.SO.CONF IIOТD IITAB IITOOLS NEТWORKS PASSWD Pf\lHTCAP PROFLE PROТOOOLS RESOLV.CON F RPC S ECUREТТY SERVICES SHELLS SYSLOG.CONF /ОРТ " CONFIG FILE FOR ADD ON APPLICATION SOFТWARE " "ROOT" /USR " SHAREAВLE AND READ.OHLY DATA " /LO CAL /VAR "VARIABLE DATA FILES" /САСНЕ "LOCA1. SOFТWARE" /В111 /GAUES /INCLUDE /LIB /UAN /SBIN /SHARE /SRC /SHARE " STATIC DATA SHAREABLE AIIONG ALL ARCHIТECТURES " /MAN "IIANUAL PAGES" /MAN1 "uвer programa•• /UAN2 ••aystem cell:9 1 ' /MAN3 "llb functiona" /UAN4 "spocial file" /UAN5 ''fil• tormeta" /UANO 11 g11111ев" /MAN7 11 misc." /UANa ••ayatem edmin." /BIN "UOST USER OOIIMANDS" /INCLUDE "STANDARD IHCLUDE FILES FOR 'С' PROG." /LIB " OBJ , BIN , LII FILES FOR PROG. AHD PACKAGES " /SBIN " НО Н ESS EN TIAL BI\IARIES" "APPLICATION САСНЕ DATA" /LIB " VARIABLE SТАТЕ INFORUATION REIIAINS AFТEfl REBOOT " /УР " DATA FOR NIS SERVICES " /LOCK /SBIN "SУSТЕМ BI\IARIES" FАSТВООТ FAS THALT FDISK FSCK GЕТТУ HAL T IFOOHFIG IHIT IIKFS IIKSWAP REBOOT ROUTE SWAPOH SWAPOFF UPDATE "LOCK FLES FOR SHARED RESOURCES" /ОРТ " VARIAВLE DATA OF PACKAGES IHS TALLED" /RUN "INFO OF SYSТEII SIHCE IТ WAS BOOTED" /ТМР "AVAJLABLE FOR PROG." /SPOOL "DATA AWAIТIIIG PROCESSING " /LPD /MQUEUE /NEWS /RWHO /UUCP /LOG "LOG FILES AND DIR" LASТLOG IIESSAGES WТUP /ТМР ''ТЕМРЕRОRУ FILES DELEТED ОН BOOTUP" /DEV "LOCATIOH OF SPECIAL OR DEVICE FLES [CONТAIHS IIAKEDEV)" /НОМЕ " USER HOIIE DIRECТORIES" /LIB " LIBRARY AND KE RHE L IIODULES" /MNT " MOUN T FILES FOR TEMPERORY FILESYSТEIIS " /ОРТ " ADO.ON APPLICATION SOFТWARE " /ROOT "HOIIE DIR. FOR ROOT USER" Navigating the File System ● Essential navigation commands: ○ ○ ○ pwd ls cd print current directory list files change directory Navigating the File System We use pathnames to refer to files and directories in the Linux file system. ● There are two types of pathnames: ○ Absolute – The full path to a directory or file; begins with / ○ Relative – A partial path that is relative to the current working directory; does not begin with / Navigating the File System ● Special characters interpreted by the shell for filename expansion: ○ ○ ○ ○ ○ ○ ~ . .. * ? TAB your home directory (e.g., /usr1/tutorial/tuta1) current directory parent directory wildcard matching any filename wildcard matching any character try to complete (partially typed) filename Navigating the File System ● Examples: ○ ○ ○ ○ ○ ○ cd /usr/local cd ~ pwd cd .. cd / ls –d pro* Change directory to /usr/local/lib Change to home directory (could just type ‘cd’) Print working (current) directory Change directory to the “parent” directory Change directory to the “root” Listing of only the directories starting with “pro” The ls Command ● Useful options for the “ls” command: ○ ls -a List all files, including hidden files beginning with a “.” ○ ls -ld * List details about a directory and not its contents ○ ls -F Put an indicator character at the end of each name ○ ls –l Simple long listing ○ ls –lR Recursive long listing ○ ls –lh Give human readable file sizes ○ ls –lS Sort files by file size ○ ls –lt Sort files by modification time (very useful!) Some Useful File Commands ● ● ● ● ● ● ● ● ● ● ● ● ● ● cp [file1] [file2] mkdir [name] rmdir [name] mv [file] [destination] rm [file] file [file] less [file] head -n N [file] tail -n N [file] ln –s [file] [new] cat [file] [file2…] tac [file] [file2…] touch [file] od [file] copy file make directory remove (empty) directory move/rename file remove (-r for recursive) identify file type page through file display first N lines display last N lines create symbolic link display file(s) display file in reverse order update modification time display file contents, esp. binary Manipulating files and directories ● Examples: ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ cd mkdir test cd test echo ‘Hello everyone’ > myfile.txt echo ‘Goodbye all’ >> myfile.txt less myfile.txt mkdir subdir1/subdir2 mkdir -p subdir1/subdir2 mv myfile.txt subdir1/subdir2 cd .. rmdir test rm –rf test # The same as cd ~ # Fails. Why? # Succeeds # Fails. Why? # Succeeds Symbolic links ● Sometimes it is helpful to be able to access a file from multiple locations within the hierarchy. On a Windows system, we might create a “shortcut.” On a Linux system, we can create a symbolic link: ○ ○ ○ mkdir foo touch foo/bar ln –s foo/bar . # make foo directory # create empty file # create link in current dir. Finding a needle in a haystack ● The find command has a rather unfriendly syntax, but can be exceedingly helpful for locating files in heavily nested directories. ● Examples: ○ ○ ○ ● find ~ -name bu –type d find . –name my-file.txt find ~ -name ‘*.txt’ # search for “bu” directories in ~ # search for my-file.txt in . # search for “*.txt” in ~ Quiz: ○ ○ Can you use find to locate a file called “needle” in your haystack directory? Extra credit: what are the contents of the “needle” file? Processes & Job Control Processes and Job Control ● As we interact with Linux, we create numbered instances of running programs called “processes.” You can use the ‘ps’ command to see a listing of your processes (and others!). To see a long listing, for example, of all processes on the system try: [username@scc1 ~]$ ps -ef ● To see all the processes owned by you and other members of the class, try: [username@scc1 ~]$ ps -ef | grep tuta Processes and job control ● Use “top” to see active processes. Tasks: 408 total, 1 running, 407 sleeping, 0 stopped, 0 zombie Cpu(s): 0.3%us, 0.1%sy, 0.0%ni, 99.6%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 99022756k total, 69709936k used, 29312820k free, 525544k buffers Swap: 8388604k total, 0k used, 8388604k free, 65896792k cached PID 7019 38246 41113 2324 7107 27409 1 2 3 4 5 USER root isw cjahnke root nobody theavey root root root root root PR 20 20 20 20 20 20 20 20 RT 20 RT NI 0 0 0 0 0 0 0 0 0 0 0 VIRT 329m 88724 13672 0 89572 26652 25680 0 0 0 0 RES 137m 2764 1512 0 10m 1380 1604 0 0 0 0 SHR 4852 1656 948 0 2400 880 1280 0 0 0 0 S %CPU %MEM TIME+ COMMAND S 4.0 0.1 217:01.56 sge_qmaster S 0.7 0.0 0:01.28 sshd R 0.7 0.0 0:00.03 top S 0.3 0.0 0:21.82 kondemand/2 S 0.3 0.0 2:18.05 gmond S 0.3 0.0 0:34.84 tmux S 0.0 0.0 0:05.74 init S 0.0 0.0 0:00.07 kthreadd S 0.0 0.0 0:00.89 migration/0 S 0.0 0.0 0:01.72 ksoftirqd/0 S 0.0 0.0 0:00.00 stopper/0 . (refreshes every 2 seconds) Foreground/background ● Thus far, we have run commands at the prompt and waited for them to complete. We call this running in the “foreground.” ● Use the “&” operator, to run programs in the “background”, ○ Prompt returns immediately without waiting for the command to complete: [username@scc1 ~]$ mycommand & [1] 54356 [username@scc1 ~]$ ← process id Process Control Practice ● Let’s look at the “countdown” script, in your scripts folder for practice [username@scc1 ~]$ cd ~/scripts [username@scc1 ~]$ cat countdown ● Make the script executable with chmod: [username@scc1 ~]$ chmod +x countdown ● First, run it for a few seconds, then kill with Control-C. [username@scc1 ~]$ ./countdown 100 100 99 98 ^C ← Ctrl-C = (^C) Process control ● Now, let’s try running it in the background with &: [username@scc1 ~]$ ./countdown 60 & [1] 54355 [username@scc1 ~]$ 60 59 ● The program’s output is distracting, so redirect it to a file: [username@scc1 ~]$ countdown 60 > c.txt & [1] 54356 [username@scc1 ~]$ Process control ● Type ‘ps’ to see your countdown process. ● Also, try running ‘jobs’ to see any jobs running in the background from this bash shell. ● To kill the job, use the ‘kill’ command, either with the five-digit process id: ○ kill 54356 ● Or, you can use the job number (use ‘jobs’ to see list) with ‘%’: ○ kill %1 Backgrounding a running job with C-z and ‘bg’ ● Sometimes you start a program, then decide to run it in the background. [username@scc1 scripts]$ ./countdown 200 > c.out ^Z [1]+ Stopped ./countdown 200 > c.out [username@scc1 scripts]$ bg [1]+ ./countdown 200 > c.out & [username@scc1 scripts]$ jobs [1]+ Running ./countdown 200 > c.out & [username@scc1 scripts]$ ← Ctrl-Z = (^Z) Editors Regular expressions ● Many Linux tools, such as grep and sed, use strings that describe sequences of characters. These strings are called regular expressions. Here are some examples: ○ ○ ○ ○ ^foo bar$ [0-9]\{3\} .*a.*e.*i.*o.*u.* # line begins with “foo” # line ends with “bar” # 3-digit number # words with vowels in order* File Editors ● gedit ○ ● nano ○ ● Lightweight editor. Non-Xwindows. emacs ○ ● Notepad-like editor with some programming features (e.g., syntax highlighting). Requires X-Windows. Swiss-army knife, has modes for all major languages, and can be customized. Formerly steep learning curve has been reduced with introduction of menu and tool bars. Can be used under Xwindows or not. vim ○ A better version of ‘vi’ (an early full-screen editor). Very fast, efficient. Steep learning curve. Popular among systems programmers. Terminal or X-Windows. Creating and Running Code “Hello, world” in C ● cd to “~/c”, and read hello.c into your editor of choice. ● Modify the text on the printf line between “[“ and “]” and save the file. ● Produce an executable file called “hello” by compiling the program with gcc: [username@scc1 ~]$ gcc –o hello hello.c ● Run the program at the command line: [username@scc1 ~]$ ./hello ● Optional: modify countdown script to run hello program