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Linux and VI Editor Fundamentals

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Objectives

This self-directed tutorial is mainly for people who have none or very little experience in Linux system, particularly for Windows users who want to migrate to SHARCNET Linux systems. Examples shown in the lightgrey areas were run on 'narwhal', a SHARCNET cluster. We hope that this tutorial would be a good starting point for newcomers to Linux.

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What is Linux?

Linux is a free Unix-type operating system originally created by Linus Torvalds with the assistance of developers around the world in the 90's. Linux is becoming popular as a powerful, low-cost operating system for cluster servers.

Linux Features
  • multitasking: several programs running at once
  • multiusers: several users at the same machine at once
  • multiplatforms: it runs on many different CPU
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Directory Structure in Linux

This is not a complete list, but the most general directories on Linux system.
Directory Meaning
/bin Directory for system command
/dev Directory with special files which enable to work with pheripheral devices
/etc System programs and data
/lib Libraries that are needed to execute the binaries in /bin/ and /sbin/
/mnt Directory for temporarily mounted file systems
/tmp Directory for temporary data sets
/usr Other system programs
/var Files which are being updated during system running
/opt Directory for large, static application software packages
/home User's home directory. User has a common home directory on SHARCNET systems
/work work directory, with a quota of 200GB on some large SHARCNET systems
/scratch scratch directory on SHARCNET systems with an expiry time of 2 weeks

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Getting Started

Let's try a few simple commands
  • login
    Use SSH (see: SSH for Windows Users) to login onto SHARCNET linux systems

  • hostname: Print system name

  • [jemmyhu@nar316 ~]$ hostname
    nar316

  • who: Print all usernames currently logged in
  •            
    

[jemmyhu@nar316 ~]$ who
inta     pts/0        Nov 29 12:10 (pharmtech4.pharm.helsinki.fi)
jemmyhu  pts/1        Nov 29 09:33 (jemmyhu.uwaterloo.ca)
jemmyhu  pts/2        Nov 29 09:34 (jemmyhu.uwaterloo.ca)
tomek    pts/3        Nov 19 10:00 (lola.hut.fi)
merz     pts/5        Nov 29 12:52 (nar317)
michaelg pts/4        Nov  2 12:47 (pc-mat1.eng.mcmaster.ca)
viv      pts/6        Nov 26 19:12 (dirac.physics.uoguelph.ca)
mhashimo pts/7        Nov 26 17:21 (lab2.apmaths.uwo.ca)
msammalk pts/8        Nov 29 11:13 (mae-msammalk.princeton.edu)
sclee    pts/9        Nov 29 14:37 (sclee.uwaterloo.ca)
merz     pts/10       Nov 29 14:41 (scinaa61.uwaterloo.ca)
mjhillie pts/12       Nov 27 10:56 (hillier.uwaterloo.ca)
zzheng   pts/14       Nov 27 11:49 (meg34.megaladon.sharcnet)
  • whoami: Print the current username

    [jemmyhu@nar316 ~]$ whoami
    jemmyhu

  • pwd: Print working (current) directory

  • [jemmyhu@nar316 ~]$ pwd
    /home/jemmyhu

  • date: Display the date & time

    [jemmyhu@nar316 ~]$ date
    Mon Nov 19 15:59:55 EST 2007

  • exit: or logout to leave the system

Changing Password

To change your Linux account password, use the command passwd

[jemmyhu@nar316 ~]$ passwd
Changing password for user jemmyhu.
Changing password for jemmyhu
(current) UNIX password:
(You will write your actual password after colon.)
New password:
(You will write your new password after colon.)
Re-type new password:
(You will repeat your new password after colon.)
Password changed

If you type your old password and a new password correctly, the new one becomes valid.

NOTE: you can change your SHARCNET password on the SHARCNET webportal.

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Basic Linux Commands

The basic format of a command is command [option] ...,
please check the command's manpage (man command) for other options.
  • ls - List the contents of a directory
    ls displays the names of all files and subdirectories in the working (current) directory. 
     
    

[jemmyhu@nar316 ~]$ ls
adf2007.01                           Dakota     mpi              script         
adf2007.01.pc64_linux.hpmpi.bin.tar  debugger   Octave_matlab    test_g03
awk_example                          fftw_test  OpenMP_Summer07  test_mpiPWSCF
bin                                  HU         overLord         util
Courses                              Matlab     scratch          work
    ls -l shows the detailed information of the contents (permissions, owners, size, and timestamp). 
     
    

[jemmyhu@nar316 ~]$ ls -l
total 352192
drwxr-xr-x   8 jemmyhu jemmyhu      4096 Nov 23 09:47 adf2007.01
-rw-rw-r--   1 jemmyhu jemmyhu 360212480 Nov 12 13:10 adf2007.01.pc64_linux.hpmpi.bin.tar
drwxr-x---   2 jemmyhu jemmyhu      4096 Apr 30  2007 awk_example
drwxr-xr-x   2 jemmyhu jemmyhu      4096 Nov  9 12:14 bin
drwx------   3 jemmyhu jemmyhu      4096 Apr 12  2007 Courses
drwxr-xr-x   4 jemmyhu jemmyhu      4096 May 29  2007 Dakota
drwx------   3 jemmyhu jemmyhu      4096 Aug 22 15:39 debugger
drwxr-x---   3 jemmyhu jemmyhu      4096 May  7  2007 fftw_test
drwx------  13 jemmyhu jemmyhu      4096 Oct 31 12:08 HU
drwxrwxr-x   2 jemmyhu jemmyhu      4096 Oct 31 11:52 Matlab
drwx------   3 jemmyhu jemmyhu      4096 Oct 30 10:57 mpi
drwx------   2 jemmyhu jemmyhu      4096 Aug 24 15:31 Octave_matlab
drwx------   6 jemmyhu jemmyhu      4096 Jun 13 11:06 OpenMP_Summer07
drwx------   2 jemmyhu jemmyhu      4096 Oct 31 11:54 overLord
lrwxrwxrwx   1 jemmyhu jemmyhu        16 Aug  1 11:22 scratch -> /scratch/jemmyhu
drwx------   2 jemmyhu jemmyhu      4096 Nov 21 12:14 script
drwx------   2 jemmyhu jemmyhu      4096 Nov  6 15:29 test_g03
drwx------   7 jemmyhu jemmyhu      4096 Jun  7 21:34 test_mpiPWSCF
drwx------   2 jemmyhu jemmyhu      4096 Oct 31 11:58 util
lrwxrwxrwx   1 jemmyhu jemmyhu        13 Aug  1 11:21 work -> /work/jemmyhu
    ls -a shows all subdirectories and files, even files that are hidden (these files begin with a dot.) 
    [jemmyhu@nar316 ~]$ ls -a
.                                    Courses          .octave_hist     test_g03             
..                                   Dakota           Octave_matlab    test_mpiPWSCF 
adf2007.01                           .ddt             OpenMP_Summer07  util             
adf2007.01.pc64_linux.hpmpi.bin.tar  .ddt_session     .pathscale       .viminfz.tmp 
.assistant                           debugger         .rpmmacros       work
awk_example                          fftw_test        scratch          .Xauthority
.bash_history                        HU               script    
.bash_logout                         .lsbatch         .sq            
.bash_profile                        Matlab           .ssh         
.bashrc                              mpi              test_g03
bin                                  .nodelist        test_mpiPWSCF
  • mkdir - Create directory (i.e., a folder) 
     mkdir my_dir 
 my_dir is the name of a newly created directory, a subdirectory of the current directory.
  • rmdir - Remove empty directory 
     rmdir my_dir 
 remove my_dir if it is empty. If my_dir is not empty, use
 rm -r my_dir
  • cd - Change directory
    cd Change to your home directory
    cd .. Change to the parent directory
    cd Directory Change to directory

    [jemmyhu@nar317 ~]$ cd
    [jemmyhu@nar317 ~]$ pwd
    /home/jemmyhu
    [jemmyhu@nar317 ~]$ cd ..
    [jemmyhu@nar317 home]$ pwd
    /home
    [jemmyhu@nar317 home]$ cd jemmyhu
    [jemmyhu@nar317 ~]$ pwd
    /home/jemmyhu

  • more, less - Display contents of File, page by page
    more File
    less File
    User can controle the output:
    • press space the next screen is displayed
    • press enter the next row is displayed
    • press q the command is finished

  • cp - Copy File
    cp File NEWFILE Copy FILE to NEWFILE in the same directory.
    cp /home/jemmyhu/File . Copy FILE from /home/jemmyhu to the current directory.
    cp -r DIR NEWDIR Copy DIR and all its contents to NEWDIR.

  • mv - Move or rename file or directory
    mv File NEWNAME Rename FILE to NEWNAME in the same directory.
    mv File DIR Move FILE to existing directory DIR.
    mv DIR NEWDIRNAME Rename DIR to NEWDIRNAME

  • rm - Remove file
    rm File Remove FILE in the current directory.
    rm b*p Remove all files beginning with b and ending with p in the current directory.
    rm * Remove all files in the current directory
    rm -i * the system will ask for permission before removing each file.
    rm -r DIR Remove DIR and its entire contents.

  • file - Determine file type

    [jemmyhu@nar316 work]$ file README
    README: ASCII English text

  • diff - Display the differences between two files
    diff File_1 File_2 Show differences between two versions of a file.

  • find - Search for files that meet a desired criteria
    find File(s) Search current dir and its subdirs for FILE(S).
    find /usr -name "lpr" -print Find a file lpr in directory /usr and its subdirectories.

    [jemmyhu@nar316 ~]$ find /usr -name "lpr" -print
    /usr/bin/lpr
    /usr/share/terminfo/l/lpr

  • ps - List processes
    ps -u username List all your processes. 
               
    

[jemmyhu@nar316 ~]$ ps -u jemmyhu
PID   TTY       TIME    CMD
11437 ?        00:00:00 sshd
11438 pts/5    00:00:00 bash
13861 pts/5    00:00:00 ps

  • kill - Stop a process from running
    kill -9 PID Stop a process with process NO. PID before it has been finished normally.

  • time - Measure program running time
    time executablecode Display the time used to run executablecode.

    [jemmyhu@nar316 ~]$ time ./pi-serial
    PI = 3.141593

    real 0m0.002s
    user 0m0.001s
    sys 0m0.002s

  • top - List processes running on the system 
               
    

[jemmyhu@nar316 ~]$ top
top - 11:46:58 up 32 days, 21:23, 18 users,  load average: 1.00, 1.02, 1.20
Tasks: 314 total,   2 running, 312 sleeping,   0 stopped,   0 zombie
Cpu(s):  1.0% us,  0.7% sy,  0.0% ni, 98.2% id,  0.0% wa,  0.0% hi,  0.2% si
Mem:   4037544k total,  4020680k used,    16864k free,     4132k buffers
Swap:  6289408k total,   257344k used,  6032064k free,  3162308k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                  
17862 mjhillie  16   0 13324 1820 1196 S  0.7  0.0   4:48.16 top                      
15146 root      18   0 62636 3692 1476 R  0.7  0.1   0:00.02 auto.home                
12647 tomek     15   0 46280 2396 1592 S  0.3  0.1   0:41.05 sshd                     
12920 tomek     15   0 46280 2400 1592 S  0.3  0.1   0:37.94 sshd                     
12921 tomek     16   0 25072 5812 1348 S  0.3  0.1   0:07.58 scp                      
15134 jemmyhu   16   0 13196 2044 1356 R  0.3  0.1   0:00.37 top                      
    1 root      16   0  4748  404  372 S  0.0  0.0   0:06.60 init
    Enter q to stop 'top' command

  • which - Locate a program file in user's path

    [jemmyhu@nar316 ~]$ which cc
    /opt/sharcnet/compile/bin/cc
    [jemmyhu@nar316 ~]$ which f90
    /opt/sharcnet/compile/bin/f90
    [jemmyhu@nar316 ~]$ which mpicc
    /opt/sharcnet/compile/bin/mpicc

  • man - Help manual 
               
    

[jemmyhu@nar316 ~]$ man sqjobs
SQJOBS(1)          User Contributed Perl Documentation             SQJOBS(1)

NAME
           sqjobs - show SQ jobs

SYNOPSIS
           sqjobs [-r][-q][-z][-v][-u user][-n][--summary][jobid...]

         options:
           -a or --all show all jobs: all users and all states
           -r          show running jobs
           -q          show queued jobs
           -z          show suspended/preempted jobs
           -l          show more detail on jobs
           -L          show more detail on jobs
           -u user     show jobs for the given user
           -n, --none  show one-line summary of cluster
           -s or --summary   show a line-per-user summary of all jobs
           -h or --help        show usage
           --man               show man page
           jobid...    one or more jobids to examine

DESCRIPTION
       sqjobs displays a succinct tabular listing of jobs in the SQ system.
    Enter q to stop 'man' command

  • df - Display free disk space 
               
    

[jemmyhu@nar316 ~]$ df
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/sda2             42441844   3662780  36623144  10% /
/dev/sda1               703596     31708    636148   5% /boot
none                   2018772         0   2018772   0% /dev/shm
/dev/sda3             27585276    966940  25217068   4% /var
10.33.1.80:/hptc_cluster
                      13938720   7976032   5254624  61% /hptc_cluster
3712500403@gm0,3712500351@gm0:/nar-sfs-mds3/client_gm
                     74565613440 41282337520 29524984824  59% /nar_sfs
10.33.1.64:/nar_home 1441960384  77531840 1291178848   6% /nar_home
10.33.1.64:/nar_data 480668576  10531008 445720992   3% /nar_data
nar_home.narwhal.sharcnet:/nar_home/mjhillie
                     1441960360  77531832 1291178832   6% /home/mjhillie
bull_home.bull.sharcnet:/bull_home/zbice
                     1441960360 250717016 1117993648  19% /home/zbice
bull_home.bull.sharcnet:/bull_home/mhashimo
                     1441960360 250717016 1117993648  19% /home/mhashimo
10.20.0.126:/bull_home/jemmyhu
                     1441960360 250717016 1117993648  19% /home/jemmyhu
10.20.0.126:/bull_home/kowalskm
                     1441960360 250717016 1117993648  19% /home/kowalskm
bull_home.bull.sharcnet:/bull_home/tomek
                     1441960360 250717016 1117993648  19% /home/tomek
wha_home.whale.sharcnet:/wha_home/wangh29
                     1441960360  99059832 1269650832   8% /home/wangh29

  • du - Display file/directory disk usage (in KB)
    du -sh DIRECTORY Display only the total disk usage of DIRECTORY (in MB). 
               
    

[jemmyhu@nar316 ~]$ pwd
/home/jemmyhu
[jemmyhu@nar316 ~]$ ls
adf2007.01                           Dakota     mpi              script        
adf2007.01.pc64_linux.hpmpi.bin.tar  debugger   Octave_matlab    test_g03
awk_example                          fftw_test  OpenMP_Summer07  test_mpiPWSCF
bin                                  HU         overLord         util 
Courses                              Matlab     scratch          work

[jemmyhu@nar316 ~]$ du mpi
3896    mpi/mpi-2/gulper
3944    mpi/mpi-2
4160    mpi

[jemmyhu@nar316 ~]$ du -sh mpi
4.1M    mpi
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File Permissions

  • chmod - Change file/directory access permissions
  • chmod who=permissions Filename Gives 'who' the specified permissions for a given filename.
    chmod who=permissions DIR Gives 'who' the specified permissions for a given directory.
    Operator = is used to set up permissions
    To add permissions, use + To take away permissions, use -

    'who' is a list of letters that specifies whom you are going to be giving permissions to.
    These may be specified in any order.
    Letter Meaning
    u user who owns the file
    g group the file belongs to
    o other users
    a all of the above (an abbreviation for ugo)

    'permissions' are the same letters that you see in the directory listing (ls -l).
    r permission to read the file
    w permission to write (or delete) the file
    x permission to execute the file 
    EXAMPLES:

[jemmyhu@nar316 work]$ ls -l README
-rw-------  1 jemmyhu jemmyhu 342 Nov  7 14:17 README

The letters written from the 2nd to the 10th column are for file permissions.
The first three columns are permissions for the user, the columns 5, 6, 7
for the user's group, and the last three for other users.

In the above example, user (jemmyhu) has read and write permissions on file 'README',
but no permissions for the group and others.

    Here are some examples to change the permissions on file 'README':

    [jemmyhu@nar316 work]$ ls -l README *View the original permissions on file 'README'
    -rw------- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README

    [jemmyhu@nar316 work]$ chmod ugo=rw README *Give read and write permissions to all
    [jemmyhu@nar316 work]$ ls -l README
    -rw-rw-rw- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README

    [jemmyhu@nar316 work]$ chmod ug+x README *Add execute permission to user and group
    [jemmyhu@nar316 work]$ ls -l README
    -rwxrwxrw- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README

    [jemmyhu@nar316 work]$ chmod ug-x README *Take away execute permission from user and group
    [jemmyhu@nar316 work]$ ls -l README
    -rw-rw-rw- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README

    [jemmyhu@nar316 work]$ chmod a-w README *Take away write permission for all
    [jemmyhu@nar316 work]$ ls -l README
    -r--r--r-- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README

    [jemmyhu@nar316 work]$ chmod u+w README *Add write permission to user
    [jemmyhu@nar316 work]$ ls -l README
    -rw-r--r-- 1 jemmyhu jemmyhu 342 Nov 7 14:17 README
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Other Important Linux Commands

  • alias - Create an alias
  • awk - Find and Replace text
  • cat - Display a short file, or used to append files
  • echo - Display message on screen
  • env - Environment variables
  • grep - Search file(s) for lines that match a given pattern
  • gzip/gunzip - Compress or decompress named file(s)
  • make - Recompile a group of programs
  • quota - Display disk usage and limits
  • tar - Tape ARchiver
  • touch - Create an empty file or Change file timestamps
  • wc - Print byte, word, and line counts
For a list of Linux commands, please see Linux Bash Commands .

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What is vi?

vi (visual editor) is the default editor that comes with the UNIX/Linux operating system. 
Alternate editors for UNIX environments include nano (formerly named pico) and emacs
(For basic emacs commands, see: http://www.cs.colostate.edu/helpdocs/emacs.html )

The vi editor is a full screen editor and has two modes of operation:
1. Command mode commands which cause action to be taken on the file, and
2. Insert mode in which entered text is inserted into the file.

In the command mode, every character typed is a command that does something to the text file
being edited; a character typed in the command mode may even cause the vi editor to enter the
insert mode. In the insert mode, every character typed is added to the text in the file; 
pressing the Esc key turns off the Insert mode.
While there are a number of vi commands, just a handful of these are usually sufficient for
beginning vi users.

Both UNIX/Linux and vi are case-sensitive. Be sure not to use a capital letter in place of a 
lowercase letter; the results will not be what you expect.
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Basic vi Commands

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Further Reading

SAMS Teach Yourself Unix in 24 Hours, third edition, Sams Publishing, 2001

http://www.fsid.cvut.cz/cz/U201/LINUX.HTML
Quick Linux Tutorial, by Jiri Vogel
http://faculty.plattsburgh.edu/jan.plaza/computing/help/commands.html
Basic Unix Commands
http://www.ss64.com/bashsyntax/vi.html
vi Editor Commands
http://www.cs.colostate.edu/helpdocs/vi.html
Basic vi Commands

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