HPC_Linux_Summer_2024.pdf

Introduction to Linux Feng Chen HPC User Services LSU HPC & LONI [email protected] Louisiana State University Baton Rouge June 26, 2024  Roadmap What is Linux, Why Linux Linux file system Basic commands File permi...

Introduction to Linux Feng Chen HPC User Services LSU HPC & LONI [email protected] Louisiana State University Baton Rouge June 26, 2024  Roadmap What is Linux, Why Linux Linux file system Basic commands File permissions Variables Commands with HPC clusters File editing Introduction to Linux 2  Why Linux for HPC OS Family System Share November 2014 November 2023 Linux is the most popular OS used in supercomputers http://www.top500.org/statistics/list/ Introduction to Linux 3  History of Linux (1) ▪ Unix was initially designed and implemented at AT&T Bell Labs 1969 by Ken Thompson, Dennis Ritchie, Douglas McIlroy, and Joe Ossanna ▪ First released in 1971 and was written in assembly language ▪ Re-written in C by Dennis Ritchie in 1973 for better portability (with exceptions to the kernel and I/O) ▪ The GNU Project by Richard Stallman started in 1983 ▪ Goal: create a “complete Unix-compatible software system” with entirely free software Introduction to Linux 4  History of Linux (2) ▪ Linus Torvalds, a student at University of Helsinki began working on his own operating system, which became the "Linux Kernel", 1991 ▪ Linus released his kernel for free download and helped further development Introduction to Linux 5  History of Linux (3) ▪ Linux as the kernel only, applications on top of the kernel were still missing ▪ The GNU Project by Richard Stallman started in 1983 -Creating a “complete Unix-compatible software system” with entirely free software ▪ "GNU/Linux”(Linux): Linux kernel + free software from the GNU project ▪ GNU/Linux (Linux) released under the GNU Public License (GPL): Free to use, modify and re-distribute if later distributions are also under GPL Introduction to Linux 6  What is Linux ▪ Essential components: Linux kernel + GNU system utilities + installation scripts + management utilities etc. ▪ Many software vendors release their own packages, known as distributions – Debian, Ubuntu, Mint – Red Hat, Fedora, CentOS, Scientific Linux – Slackware, OpenSUSE, SLES, SLED – Gentoo ▪ Linux distributions offer a variety of desktop environment Redhat, KDE, GNOME, XFCE, LXDE, Cinnamon, MATE Introduction to Linux 7 Redhat Desktop Introduction to Linux 8 Ubuntu Desktop Introduction to Linux 9 CentOS GNOME Desktop Introduction to Linux 10 Debian MATE Desktop Introduction to Linux 11 Linux System Architecture Introduction to Linux 12  Linux Kernel What is a Kernel The core component of an OS Manage the system’s resources, memory, file systems… Provide the lowest level abstraction layer to upper layer components Inter-process communications and system calls are used to make services available The kernel is so named because - like a seed inside a hard shell - it exists within the OS and controls all the major functions of the hardware, whether it’s a phone, laptop, server, or any other kind of computer. Introduction to Linux 13  Linux Shell What is a Shell ▪ An application running on top of the kernel and provides a powerful interface to the system ▪ Process user’s commands, gather input from user and execute programs ▪ Types of shell with varied features ▪ sh ▪ csh Each shell has a default prompt. For the 5 most common shells: ▪ ksh ▪ bash $ (dollar sign) - sh, ksh, bash ▪ tcsh % (percent sign) - csh, tcsh Introduction to Linux 14  Shell Comparison Software sh csh ksh bash tcsh Programming language y y y y y Shell variables y y y y y Command alias n y y y y Command history n y y y y Filename autocompletion n y* y* y y Command line editing n n y* y y Job control n y y y y *: not by default http://www.cis.rit.edu/class/simg211/unixintro/Shell.html Introduction to Linux 15  Shell Comparison Software sh csh ksh bash tcsh Programming language y y y y y Shell variables y y y y y Command alias n y y y y Command history n y y y y Filename autocompletion n y* y* y y Command line editing n n y* y y Job control n y y y y *: not by default http://www.cis.rit.edu/class/simg211/unixintro/Shell.html Introduction to Linux 16  The command sudo apt update is commonly used in Linux systems (especially Debian-based distributions like Ubuntu) to update the package list from the repositories. Linux Applications Let's break it down: Explanation: sudo: sudo stands for superuser do. It gives you temporary ▪ GNU compilers, e.g., gcc, gfortran administrative (root) privileges, allowing you to run commands that require higher permissions. In this case, updating package lists typically requires administrative access, so sudo is used to execute the command with those privileges. ▪ OpenOffice apt: apt stands for Advanced Package Tool. It is a package management system used to install, update, and remove software on Debian-based Linux distributions. ▪ Editors, e.g., vim, emacs apt interacts with the package manager to download or install software from repositories. update: The update command refreshes the package index or ▪ parallel package list on your system. It contacts the repositories (online sources where software packages are stored) and fetches the latest versions of package information, such as the latest available versions, security patches, and other updates. ▪ wget Important Note: apt update does not install or upgrade any software; it simply downloads the latest package lists to ensure your system knows about the latest available software. What happens when you run sudo apt update: ▪ cat, ls, cp The system checks the online repositories listed in your system's configuration (usually in /etc/apt/sources.list and related files). …. It fetches the most recent list of packages and their versions. This helps your system become aware of the latest software updates or new packages. https://directory.fsf.org/wiki/GNU Introduction to Linux 17  What can you do with a shell? ▪ Check the current shell ▪ echo $SHELL ▪ List available shells on the system ▪ cat /etc/shells ▪ Change to another shell ▪ exec sh ▪ Date and time ▪ date ▪ wget: get online files ▪ wget https://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.gz ▪ Compile and run applications ▪ gcc hello.c –o hello ▪./hello Introduction to Linux 18  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 19  Files ▪ One of the defining features of Linux and other UNIX-like operating systems is that “everything is a file.” ▪ All data in Linux/UNIX are organized in a file format ▪ A file is a collection of data created by users, system admins... ▪ Documents composed of ascii text ▪ Program written in high level programming languages ▪ Executables that you can run ▪ Directory containing information about its content Introduction to Linux 20  File Directory Structure ❖ All files are arranged in directories. ❖ These directores are organized into the file system bin boot dev etc home lib mnt tmp usr var work user1 user2 ·· user1 user2 ·· · Desktop · bin lib local include share Documents Downloads compilers packages ·· Public · ·· Intel amber · GNU python ·· · ·· · Introduction to Linux 21  Important Directories contains files that are essential for system operation, available for use by all /bin users. contains libraries that are essential for system operation, available for use by /lib,/lib64 all users. /var used to store files which change frequently (system level not user level) /etc contains various system configurations /dev contains various devices such as hard disk, CD-ROM drive etc /sbin same as bin but only accessible by root /tmp temporary file storage /boot contains bootable kernel and bootloader /usr contains user documentations, binaries, libraries etc contains home directories of all users. This is the directory where you are at /home when you login to a Linux/UNIX system. Introduction to Linux 22  File Path Definition: position/address in the directory tree ▪ Absolute path ▪ Uniquely defined and does NOT depend on the current path ▪ Start with "/" ▪ E.g., /tmp is unique ▪ Relative path ▪ Depend on the current location in the directory tree ▪ Does not start with "/" ▪. is the current working directory ▪.. is one directory up ▪ E.g.,../tmp is not unique Introduction to Linux 20  Linux is Case Sensitive ▪ All names are case sensitive ▪ Commands, variables, files etc. ▪ Example: MyFile.txt, myfile.txt, MYFILE.TXT are three different files in Linux Introduction to Linux 24  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 25  Basic Commands ▪ Command format: command_name [options] arguments ls –l /home/$USER ▪ Command prompt: a sequence of characters used in a command line interface to indicate the readiness to accept commands ▪ Prompt user to take action ▪ A prompt usually ends with one of the characters $,%#,:,> and often includes information such as user name and the current working directory ▪ The format can be changed via $PS1 Introduction to Linux 26  Get More Information ▪ Man: show the manual for a command or program ▪ The manual shows how to use the command and list the different options and arguments ▪ Usage: man ▪ Example: man ls ▪ Apropos: show all of the man pages that may be relevant to a certain command or topic ▪ Usage: apropos ▪ Example: apropos editor ▪ Info: Information of documents ▪ info ls Introduction to Linux 27  Commands: pwd and cd ▪ pwd:print the current working directory ▪ Usage: pwd ▪ Example: pwd ▪ cd :allow one to change the current working directory ▪ Usage: cd [destination] ▪ Example: cd /tmp ▪ The default destination is the home directory if [destination] is omitted ▪ ~ stands for home directory (bash) Introduction to Linux 28  Commands: ls ▪ ls command list the contents of a directory ▪ Usage: ls ▪ Example: ls ▪ The default path will be current working directory if path is omitted. ▪ Options ▪ -l: show long listing format ▪ -a: (--all) show hidden files(name starts with an “.” is hidden) ▪ -r: reverse order when sorting ▪ -t: show modification times ▪ -h: (--human-readable) use file sized in SI units (bytes, kbytes, megabytes etc.) ▪ -d: (--directory) list directory entries instead of contents, and do not dereference symbolic links Introduction to Linux 29  Commands: cat, more/less, head/tail ▪ Display the content of a file to screen ▪ cat: show content of a file ▪ more: display contents one page at a time ▪ less: display contents one page at a time, and allow forward/backward scrolling ▪ Usage: cat/more/less ▪ head: output the first part of files ▪ tail: output the last part of files ▪ Usage: head/tail ▪ Be careful when using those commands on binary files – file: reveal what type of file the target is Introduction to Linux 30  Auto-completion ▪ Allows automatic completion of typing file, directory or command name via the TAB key ▪ Convenient, also error-proof ▪ If there is no unique name, all matching names will show ▪ The default feature in bash and tcsh ▪ Example: your home directory contains directories Desktop, Documents and Downloads – Enter command ls D, then press tab – Enter command ls Do, then press tab – Enter command ls Dow, then press tab Introduction to Linux 31  Wildcards Linux allows the use of wildcards for strings – *: any number of characters Example: ls *.gz will list all the file ending with.gz – ?: any single character – [ ]: specify a range e.g.: ls test[1-9]list the file test1,test2 … Introduction to Linux 32  Commands: mkdir ▪ mkdir:create a directory ▪ Usage: mkdir ▪ Example: mkdir ~/testdir ▪ By default, the directory is created in the current directory ▪ Options -p: create the target directory as well as any directories that appear in the path but does not exist Introduction to Linux 33  Commands: cp ▪ cp:copy a file or directory ▪ Usage: cp ▪ Example: cp $HOME/.bashrc ~/testdir ▪ Options ▪ -r: copy recursively, required when copying directories. ▪ -i: prompt if file exists on destination and can be copied over. ▪ -p: preserve file access times, ownership etc. ▪ By default cp will overwrite files with identical names (!!) ▪ If there are more than one source files, then the destination must be a directory Introduction to Linux 34  Commands: rm ▪ rm: removes files and directories ▪ Usage: rm ▪ Examples: rm testdir/.bashrc ~/testfile ▪ Options ▪ -r: remove recursively, required when deleting directories ▪ -i: prompt if the file really needs to be deleted ▪ -f: force remove (override the -i option) ▪ BE CAREFUL: DELETED FILES *CANNOT* BE RECOVERED!!! Introduction to Linux 40  Commands: mv ▪ mv:moves or renames a file or directory ▪ Usage: mv ▪ Example: mv test test1 ▪ Use the –i option to prompt if a file or directory will be overwritten. ▪ If there are more than one source files, the destination must be a directory Introduction to Linux 36  Commands: alias ▪ alias: create a shortcut to another command or name to execute a long string ▪ Usage ▪ bash/sh/ksh: alias =“” ▪ csh/tcsh: alias “” ▪ Example ▪ bash/sh/ksh: alias lla=“ls –altr” ▪ csh/tcsh: alias lls “ls –altr” ▪ alias can be used to prevent files from being deleted accidentally – Example: alias rm “rm –i” ▪ alias: list all aliases currently defined (without arguments) ▪ unalias: remove an alias Introduction to Linux 37  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 38 File Permission Introduction to Linux 39  Linux File Permission ▪ Designed as the multiuser environment, the access restriction of files to other users on the system is embedded. ▪ Three types of file permission ▪ Read (r) ▪ Write (w) ▪ Execute (x) ▪ Three types of user ▪ User (u) (owner) ▪ Group (g) (group members) ▪ World (o) (everyone else on the system) Introduction to Linux 40  Linux File Permission Each file in Linux has the following attributes: Owner permissions: determine what actions the owner of the file can perform on a file Group permissions: determine what actions a user, who is a member of the group that a file belongs to, can perform on a file Other (world) permissions: indicate what action all other users can perform on a file Introduction to Linux 41  File Permission The first column indicates the type of a file/dir/link – d: for directory – l: for symbolic link – -: for normal file Introduction to Linux 42  File Permission Owner Group Others (u) (g) (o) Introduction to Linux 43  Changing File Permission ▪ chmod is a *NIX command to change permissions on a file ▪ Usage: chmod ▪ –R: change permission recursively in a directory ▪ chmod in Symbolic Mode: Chmod operator Description + Adds the designated permission(s) to a file or directory. - Removes the designated permission(s) from a file or directory. = Sets the designated permission(s). e.g. chmod u+rwx filename chmod o-w filename Introduction to Linux 44  Changing File Permission ▪ chmod in Absolute Mode: Number Octal Permission Representation Ref 0 No permission --- 1 Execute permission --x 2 Write permission -w- 3 Execute and write permission: 1 (execute) + 2 (write) = 3 -wx 4 Read permission r-- 5 Read and execute permission: 4 (read) + 1 (execute) = 5 r-x 6 Read and write permission: 4 (read) + 2 (write) = 6 rw- 7 All permissions: 4 (read) + 2 (write) + 1 (execute) = 7 rwx e.g. chmod 755 test.txt (u) (g) (o) Introduction to Linux 45  Permission Effect on File vs Directory Permission File Directory r read the file content ls files under the directory w write to the file create new files and directories,delete existing files and directories, rename and move the existing files and directories x execute the file cd into the directory (if executable) Introduction to Linux 46  User Groups at HPC/LONI ▪ Users are organized into groups ▪ groups command to find your group membership ▪ Group membership makes sharing files with members of a group easy ▪ Each user is in at least one group and can be in multiple groups ▪ Groups in LONI systems: lsuusers, latechusers, unousers, ullusers, sususers, tulaneusers, loniusers, xavierusers ▪ Groups in LSU HPC system Users, Admins, xsede… ▪ You are only in one of the above groups due to software licensing Introduction to Linux 47  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 48  Variables ▪ Linux allows the use of variables ▪ Similar to programming languages ▪ Number, character or string ▪ Rules for variable names ▪ Must start with a letter or underscore ▪ Number can be used anywhere else ▪ Do not use special characters such as @,#,%,$ ▪ Case sensitive ▪ Allowed: VARIABLE, VAR1234able, var_name, _VAR ▪ Not allowed: 1var, %name, $myvar, var@NAME ▪ Two types of variables: ▪ Global variables (ENVIRONMENT variables) ▪ Local variables (user defined variables) Introduction to Linux 49  Global Variables ▪ Environment variables provide a simple way to share configuration settings between multiple applications and processes in Linux ▪ Using all uppercase letters ▪ Example: ▪ PATH, LD_LIBRARY_PATH, HOME etc. ▪ To reference a variable, prepend $ to the name of the variable ▪ Example: $PATH, $LD_LIBRARY_PATH, $DISPLAY etc. ▪ printenv/env list the current environmental variables in your system. Introduction to Linux 50  List of Some Environment Variables PATH is an environmental variable in Linux and other Unix-like operating systems that tells the shell which directories to search for executable files (i.e., PATH ready-to-run programs) in response to commands issued by a user. It is widely considered to be the single most important environmental variable. LD_LIBRARY_PATH colon-separated set of directories where libraries should be searched for first HOME indicate where a user's home directory is located in the file system. PWD contains path to current working directory. OLDPWD contains path to previous working directory. TERM specifies the type of computer terminal or terminal emulator being used SHELL contains name of the running, interactive shell. PS1 default command prompt PS2 Secondary command prompt HOSTNAME The systems host name USER Current logged in user's name DISPLAY Network name of the X11 display to connect to, if available. Introduction to Linux 51  Editing Variables ▪ Assign values to variables Type sh/ksh/bash csh/tcsh Shell (local) name=value set name=value Environment (global) export name=value setenv name value ▪ Shell variables is only valid within the current shell, while environment variables are valid for all subsequently opened shells. ▪ Example: useful when running a script, where exported variables (global) at the terminal can be inherited within the script. ▪ $ export v1=one ▪ $ bash ▪ $ echo $v1 → one Introduction to Linux 52  Editing Variables at the curent login Example: to add a directory to the PATH variable sh/ksh/bash: export PATH=/path/to/executable:${PATH} csh/tcsh: setenv PATH /path/to/executable:${PATH} ▪ Path order matters, first in line takes a higher priority Introduction to Linux 53  Persistent variables for each login ▪ Not to change at each login ▪ Make setting changes available in both login and non-login shells ▪ Define these variables in the ~/.bashrc file. ▪ vim ~/.bashrc ▪ source ~/.bashrc Introduction to Linux 54  Input & Output Commands The basis I/O statements: ▪ echo: display info to screen ▪ The echo arguments command will print arguments to screen or standard output, where arguments can be a single or multiple variables, string or numbers ▪ read: reading input from screen/keyboard/prompt ▪ The read statement takes all characters typed until the Enter key is pressed ▪ Usage: read ▪ Example: read name Introduction to Linux 55  Input & Output Commands ▪ Examples ▪ echo “hello !” ▪ hello ▪ By default, echo eliminates redundant whitespaces (multiple spaces and tabs) and replaces it with a single whitespace between arguments. ▪ To include redundant whitespace, enclose the arguments within single/double quotes ▪ To expand variables, enclose the arguments with double quotes Introduction to Linux 56  Other Useful Commands passwd Change password (does not work on LSU HPC and LONI systems) chsh Change default shell (does not work on LSU HPC and LONI systems) df Report disk space usage by filesystem Estimate file space usage - space used under a particular directory or files du on a file system. sudo Run command as root (only if you have access) mount Mount file system (root only) umount Unmount file system (root only) shutdown Reboot or turn off machine (root only) top Produces an ordered list of running processes free Display amount of free and used memory in the system find Find a file alias enables replacement of a word by another string Introduction to Linux 57  Other Useful Commands vi Edit a file using VI/VIM emacs Edit a file using Emacs file Determine file type wc Count words, lines and characters in a file wc -l file grep Find patterns in a file grep alias file awk File processing and report generating awk ’{print $1}’ file sed Stream Editor sed ’s/home/HOME/g’ file set manipulate environment variables set -o emacs touch change file timestamps or create file if not present date display or set date and time which Location of a command Introduction to Linux 58  Other Useful Commands ln Link a file to another file ln -s file1 file2 wait Wait for each specified process and return its termination status. which Shows the full path of (shell) commands who Show who is logged on whoami Print effective userid finger User information lookup program whatis Display manual page descriptions history Display the command history list with line numbers. An argument of n lists only the last n lines. ❑ man command: learn more about these commands Introduction to Linux 59  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 60  Login Remote Systems ▪ Most Linux systems allocate secure shell connections from other systems ▪ Log in using the ssh command to the LSU HPC and LONI clusters ▪ Usage: ssh @ ▪ Example: ssh [email protected] ▪ –X option: forward the display of an application ▪ The default port is 22 for ssh ▪ ssh –p @ Introduction to Linux 61  File Transfer between Two Systems ▪ scp : copy files between two hosts over the ssh protocol ▪ Usage: ▪ scp @:/path/to/source @:/path/to/destination ▪ If the username is the same on both systems, omit ▪ If transferring files from or to localhost, @: option can be omitted ▪ Options are –r and –p, same meaning with cp ▪ Examples ▪ scp [email protected]:/home/user/file1. ▪ scp –r file [email protected]:/home/user Introduction to Linux 62  File Transfer between Two Systems ▪ rsync is another utility for file transferring ▪ Usage: rsync ▪ Delta-transfer algorithm ▪ Only transfer the bits that are different between source and destination ▪ Widely used for backups and mirroring as an improved copy command for everyday use ▪ Command options ▪ -a: archive mode ▪ -r: recursive mode ▪ -v: increase verbosity ▪ -z: compress files during transfer ▪ -u: skip files that are newer on the receiver ▪ -t: preserve modification times Introduction to Linux 63 Compressing and Archiving a single file Reduce storage usage or bandwidth while transferring files. ▪ Compress: gzip, zip, bzip2 ▪ Decompress: gunzip, unzip, bunzip2 ▪ Options ▪ Recursively, use the –r option ▪ Overwrite files while compressing/uncompressing, use the –f option ▪ By convention ▪ gzipped files:.gz,.z or.Z ▪ zipped files:.Zip or.zip ▪ bzipped files:.bz2 or.bz Introduction to Linux 64  Compressing and Archiving Files ▪ tar: create and manipulate streaming archived files. ▪ Usage: tar ▪ tar archived file, usually with extension.tar ▪ files/directories being archived ▪ Common options ▪ -c: create/compress an archive file ▪ -x: extract/decompress an archive file ▪ -t: list contents of archive (for testing) ▪ -z: filter the archive through gzip ▪ -j: filter the archive through bzip2 ▪ -f: archive ▪ -v: verbosely list files processed Introduction to Linux 65  Compressing and Archiving Files tar: create and manipulate streaming archived files. Examples: ▪ File compressing ▪ tar czvf file.tgz ${HOME}/* ▪ tar cjvf file.tgz2 ${HOME}/* ▪ File decompressing ▪ tar xzvf file.tgz –C [dest] ▪ tar xjvf file.tgz2 –C [dest] File listing tar tvf file.tgz Introduction to Linux 66  Pipes ▪ Pipe commands: connect two or more commands together using “|” ▪ grep: searches certain patterns from a file(s) cat file | grep [option] pattern Option Description -v Print all lines not match pattern -n Print the matched line and line number -l Print only the names of files with matching pattern -i Match either upper- or lowercase. -c Print the count of matching lines Introduction to Linux 67  Pipes: sort, wc, more, less ▪ sort: arranges lines of text alphabetically or numerically ▪ ls |sort –k2 Option Description -n Sort numerically -r Reverse the order of sort -k Sort by a certain column -t Field separator ▪ ls |wc ▪ cat file | more ▪ Cat file | less Introduction to Linux 68  I/O Redirection ▪ Three file descriptors for I/O streams (everything is a file in Linux) ▪ I/O redirection allows users to connect applications ▪ : save STDOUT to a file ▪ >>: append STDOUT to a file Introduction to Linux 69  I/O Redirection Examples ▪ Write STDOUT to file: ▪ ls –l xxx > ls.out ▪ Write STDERR to file: ▪ ls xxx 2 > ls.err ▪ Write STDERR and STDOUT to file: ▪ ls –l xxx >output 2>&1 ▪ Discard STDOUT and STDERR: command > /dev/null 2>&1 Introduction to Linux 70  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 71  Processes ▪ Process: an instance of a running program ▪ Linux create and start a new process (PID) for each command ▪ ps or top ▪ A process cab be run in : ▪ Foreground: the command prompt is not returned until the current process has finished executing. ▪ Background: the command prompt back to do some other useful work e.g. ls –l & Introduction to Linux 72  Processes and Jobs ▪ Two ways to send a job into the background: 1. command & 2. suspend a running job using Ctrl-z and bg. ▪ When a process is running in background or suspended, it will be entered on to a list along with a job number (not PID) jobs –l ▪ nohup:prevent background jobs to be terminated when users exit the shell nohup program & Introduction to Linux 73  Managing Processes and Jobs ▪ Restart a suspended job in foreground or background ▪ fg % ▪ bg % ▪ To kill or terminate a process: ▪ Job running in foreground: Ctrl-c ▪ Job whose job ID you know: kill % ▪ Job whose PID you know: kill Introduction to Linux 74  Roadmap What is Linux Linux file system Basic commands File permissions Variables Use HPC clusters Processes and jobs File editing Introduction to Linux 75  File Editing ▪ Most commonly used editors on Linux/Unix systems ▪ nano (if you only have slight edit requirements) ▪ vi or vim (vi improved) ▪ Emacs ▪ vi/vim is installed by default on Linux/Unix systems and has only a command line interface (CLI). ▪ Emacs has both a command line interface (CLI) and a graphical user interface (GUI). ▪ use emacs –nw to open file in console ▪ Other editors: nano, pico, kate, gedit, gvim, kwrite, nedit Introduction to Linux 76  File Editing (vi) vi works in two modes: – Command mode This is the mode when entering vi Commands can be issued at the bottom of the screen, e.g. copy, paste, search, replace etc. Press “i” to enter editing mode – Editing mode Text can be entered in this mode Press “esc” key to go back to the command mode Introduction to Linux 77  Most used commands (vi) Description Command Insert at cursor i Insert at the beginning of line I Delete a line dd Copy a line yy Paste p Search forward /pattern Search backward ?pattern Search again n Go to line #n n Replace text %s/new/old/g Save and exit wq Introduction to Linux 78  Editor cheatsheet (1) 0 0 Introduction to Linux 79 Editor cheatsheet (2) Introduction to Linux 80 Editor cheatsheet (3) Introduction to Linux 81  Shell Scripts ▪ Script: a program written for a software environment to automate execution of tasks ▪ A series of shell commands put together in a file ▪ When the script is executed, those commands will be executed one line at a time automatically ▪ The majority of script programs are “quick and dirty”, where the main goal is to get the program written quickly ▪ May not be as efficient as programs written in C and Fortran Introduction to Linux 82  Script Example (~/.bashrc) #.bashrc # Source global definitions if [ -f /etc/bashrc ]; then. /etc/bashrc fi # User specific aliases and functions export PATH=$HOME/packages/eFindsite/bin:$PATH export LD_LIBRARY_PATH=$HOME/packages/eFindsite/lib:$LD_LIBRARY_PATH alias qsubI="qsub -I -X -l nodes=1:ppn=20 -l walltime=01:00:00 –A my_allocation“ alias lh="ls -altrh" Introduction to Linux 83  Getting Help ▪ User Guides ▪ LSU HPC: http://www.hpc.lsu.edu/docs/guides.php#hpc ▪ LONI: http://www.hpc.lsu.edu/docs/guides.php#loni ▪ Documentation: http://www.hpc.lsu.edu/docs ▪ Archived HPC training:http://www.hpc.lsu.edu/training/archive/tutorials.php ▪ Contact us ▪ Email ticket system: [email protected] ▪ Telephone Help Desk: 225-578-0900 Introduction to Linux 84  Upcoming Trainings July 3,2024: HPC User Environment 1 July 10,2024: HPC User Environment 2 July 24,2024: LONI QB4 Launch Workshop July 31,2024: Basic Shell Scripting Introduction to Linux 85  Exercise (1) Login to a Linux machine and open a terminal Enter the following commands for pratice Understand what you are doing and ask for help if unsure. Some commands are incorrect or will fail; if this is the case, enter the correct ones Introduction to Linux 86  Exercise (1) $ echo hello world $ pwd $ whoami $ cd /tmp $ cd ~ (cd /home/uid) $ mkdir -p test/testagain $ cd test/testagain $ touch test.txt ❖ Go back to your home directory ❖ Figure out which shell you are using Introduction to Linux 87  Exercise (2) Create an alias for removing files which prompt for confirmation and delete the file that you created. From your home directory get a list of files and directory in long format in reverse order with file sizes listed in human readable format. Find out the location of vi, emacs, perl and ifort. (hint: which xxx) Change the permission of the testagain directory to be world writable. Open a few applications of choice in foreground one by one and then suspend them Get a list of suspended jobs, foreground job 1 and close it Background job 2,Kill job 3, put job 2 in foreground and close it Check if you still have any jobs running. Introduction to Linux 88  Exercise (4) If you have never used vim or emacs, go through the vim tutorial: vimtutor =============================================================================== = W e l c o m e t o t h e V I M T u t o r - Version 1.7 = =============================================================================== Vim is a very powerful editor that has many commands, too many to explain in a tutor such as this. This tutor is designed to describe enough of the commands that you will be able to easily use Vim as an all-purpose editor. Introduction to Linux 89