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Kamiak User's Guide

Commands

Basic Linux Commands

Here is a curated list of the most common Linux commands you will use. This list is by no means extensive, but these commands will allow you to navigate the clusters as well as create, destroy, and manipulate files and directories.

man

Display online manual pages. Most Linux commands have a manual page with detailed instructions on use. Replace <command name> below with command you would like information on.

-bash-4.2$ man <command name>

pwd

On a *nix system, directories are containers for files and objects. The pwd command lists the present working directory. This is the “where am I?” command.

-bash-4.2$ pwd
/home/wsuNID

cd

The cd command changes directory.

-bash-4.2$ cd NextDirectoryDown 
-bash-4.2$ pwd 
/home/wsuNID/NextDirectoryDown

As you can see, NextDirectoryDown is a subdirectory of wsuNID. And wsuNID is itself a subdirectory of home, which is a subdirectory of the root directory (/). Thus, the directories form a downward facing tree with all directories stemming from the root directory. You can move one level up in the tree by typing cd ..

-bash-4.2$ pwd 
/home/wsuNID/NextDirectoryDown
-bash-4.2$ cd .. 
-bash-4.2$ pwd 
/home/wsuNID

And you can navigate using either relative or absolute paths. That is, you can enter directory paths relative to your current location, or you can entire the entire path starting with the root directory.

-bash-4.2$ pwd 
/home
-bash-4.2$ cd wsuNID/NextDirectoryDown
-bash-4.2$ pwd 
/home/wsuNID/NextDirectoryDown
-bash-4.2$ cd /home
-bash-4.2$ pwd 
/home

Lastly, if you ever get lost you can use the tilde (~) to return to your HOME directory.

-bash-4.2$ cd ~
-bash-4.2$ pwd 
/home/wsuNID

ls

The ls command will list files in the current directory.

-bash-4.2$ ls 
a.out code.c Makefile

If you would like to see if a directory contains a specific file, you can pass the directory path and file name to ls as an argument

-bash-4.2$ ls a.out 
a.out

Setting the -l flag will display files along with their permissions and ownership.

-bash-4.2$ ls -l
total 0
-rw-r--r-- 1 wsuNID MyGroup 0 Aug 14 10:57 a.out
-rw-r--r-- 1 wsuNID MyGroup 0 Aug 14 10:57 code.c
-rw-r--r-- 1 wsuNID MyGroup 0 Aug 14 10:57 Makefile

mkdir

Create new directory.

-bash-4.2$ cd testdir
-bash: cd: testdir: No such file or directory
-bash-4.2$ mkdir testdir
-bash-4.2$ cd testdir
-bash-4.2$ pwd
/home/wsuNID/testdir

rm

Remove files and directories. CAUTION: THERE IS NO UNDOING THIS COMMAND.

-bash-4.2$ rm testfile

If you would like to remove a directory and all of its contents use the following command:

-bash-4.2$ rm -ri testdir
rm: descend into directory `testdir'? y
rm: remove regular empty file `testdir/Makefile'? y
rm: remove regular empty file `testdir/code.c'? y
rm: remove regular empty file `testdir/a.out'? y
rm: remove directory `testdir'? y
-bash-4.2$ 

The r flag specifies to remove files/directories recursively. i specifies to prompt before deleting each file.

If you are confident with the command line and your understanding of file locations you can use the f flag instead of i to force deletion of all files without prompting:

-bash-4.2$ rm -rf testdir
-bash-4.2$ ls testdir
ls: cannot access testdir: No such file or directory

rmdir

Removes directories. The rmdir is a safer approach than using rm -r as it will only act on empty directories.

-bash-4.2$ ls NextDirectoryDown/
file.txt
-bash-4.2$ rmdir NextDirectoryDown/
rmdir: failed to remove `NextDirectoryDown/': Directory not empty
-bash-4.2$ rm NextDirectoryDown/file.txt 
-bash-4.2$ rmdir NextDirectoryDown/
-bash-4.2$ ls
-bash-4.2$ 

cp

Copy file to new location.

In the example below sourcefile already exists, and destinationfile may or may not exist and will become a copy of sourcefile.

-bash-4.2$ cp sourcefile destinationfile

To copy a directory and all of its contents we use the recursive flag -r:

-bash-4.2$ cp -r sourcedir destinationdir

Take note of the order here: source first, destination second. This is the standard order across most *nix commands.

mv

Move a file to a new location.

-bash-4.2$ mv file1 file2
-bash-4.2$ ls file1
ls: cannot access file1: No such file or directory
-bash-4.2$ ls file2
file2

Unlike cp, the mv command does not create a second instance of the file or directory.

cat

Print the entire contents of a file (short for conCATenate).

-bash-4.2$ cat daysofweek.txt
monday
tuesday
wednesday
thursday
friday
saturday
sunday

tail

Displays lines from the end of a file. Useful for viewing recent results in an output file.

-bash-4.2$ cat animals
dog
Dog
cat
Racoon
DOG
bullfrog
Little Doggie

-bash-4.2$ tail -3 animals
DOG
bullfrog
Little Doggie

The -f flag can be used to tail a file interactively. New additions to the end of the file will be printed to your screen.

head

head is much like tail, except it prints from the top of a file.

-bash-4.2$ head -2 animals
dog
Dog

more

more is like cat, except it prints the file one page at a time. The spacebar is used to continue on to the next page.

Advanced Linux Commands

Star Wildcard

Shell commands can often make use of the wildcard characters. The most universal of these is the asterisk or star wildcard, *. This acts as a stand-in for any and all strings.

ls again

Suppose we have a directory containing many files, but we only want to list files ending with the .txt extension. We can use the * wildcard to request a list of any file ending in .txt

-bash-4.2$ ls
a.out  NextDirectoryDown helloworld.c  textfile01.txt  textfile02.txt
-bash-4.2$ ls *.txt
textfile01.txt  textfile02.txt
-bash-4.2$ 

Additionally, the behavior of the ls command can be modified by the addition of option flags. By default ls does not list any “hidden” files and subdirectories. To display all files and subdirectories one must add the -a flag.

-bash-4.2$ ls -l
total 4
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 a.out
drwxr-xr-x 2 wsuNID workshop 4096 Aug 18 21:37 NextDirectoryDown
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 helloworld.c
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile01.txt
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile02.txt
-bash-4.2$ ls -al
total 56
drwx------ 6 wsuNID workshop 4096 Aug 18 20:03 .
drwxr-xr-x 5 root     root     4096 Aug 12 13:00 ..
-rw------- 1 wsuNID workshop  107 Aug 18 16:59 .bash_history
-rw-r--r-- 1 wsuNID workshop   18 Jul 18  2013 .bash_logout
-rw-r--r-- 1 wsuNID workshop  176 Jul 18  2013 .bash_profile
-rw-r--r-- 1 wsuNID workshop  124 Sep 30  2014 .bashrc
-rw-r--r-- 1 wsuNID workshop  500 May  7  2013 .emacs
drwxr-xr-x 2 wsuNID workshop 4096 Nov 11  2010 .gnome2
-rw-r--r-- 1 wsuNID workshop  171 Aug  6  2014 .kshrc
drwxr-xr-x 4 wsuNID workshop 4096 Aug  6  2014 .mozilla
drwxr-xr-x 2 wsuNID workshop 4096 Aug 18 16:17 NextDirectoryDown
drwx------ 2 wsuNID workshop 4096 Aug 13 16:18 .ssh
-rw------- 1 wsuNID workshop 1786 Aug 18 20:03 .viminfo
-rw------- 1 wsuNID workshop   54 Aug 13 16:18 .Xauthority
-bash-4.2$ 

quota

Display disk quotas.

The ‘-s’ flag translates the output into a readable format. If your blocks column is equal to or greater than the quota column, you have exceeded your available disk space.

-bash-4.2$ quota -s
Disk quotas for user wsuNID (uid 12345): 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
master.10ge.cluster:/home
                  6459M  10000M  10000M           23260    250k    250k        
master.10ge.cluster:/share/apps
                  6459M  10000M  10000M           23260    250k    250k      

grep

Find text in a file. grep will return every line in the file that matches your search term.

-bash-4.2$ cat animals
dog
Dog
cat
Racoon
DOG
bullfrog
Little Doggie

-bash-4.2$ grep dog animals
dog

Use the -v flag to print out every line excluding those containing the search term. Notice that “dog” (lowercase) is missing from the results.

-bash-4.2$ grep -v dog animals
Dog
cat
Racoon
DOG
bullfrog
Little Doggie

The -i flag will search without case-sensitivity.

-bash-4.2$ grep -i dog animals
dog
Dog
DOG
Little Doggie

The -i and -v flag can be combined to exclude all lines containing the search term regardless of capitalization.

-bash-4.2$ grep -iv dog animals
cat
Racoon
bullfrog

find

Searches for files in a directory hierarchy. The find takes a directory as an argument and will search in that directory and all of it’s subdirectories for files that match the search criteria. If no directory is specified, the current directory is used.

You can search for a file by name using the -name flag as your search criteria

-bash-4.2$ find /home/wsuNID/ -name file1.txt
/home/wsuNID/dir1/file1.txt
-bash-4.2$ 

One can also search for all files that have a string of text in any portion of their name by using the star wildcard, e.g. we can find all the .txt files in our HOME directory and it’s subdirectories. Note that quotes are required around our criteria as we are now using a regular expression

-bash-4.2$ find /home/wsuNID/ -name "*.txt"
/home/wsuNID/textfile02.txt
/home/wsuNID/dir1/file1.txt
/home/wsuNID/examples/alphabet.txt
/home/wsuNID/examples/numbers.txt
/home/wsuNID/textfile01.txt
-bash-4.2$ 

These are just a couple examples of the many ways find can be used. A nice short tutorial on find with a lot of examples can be found at http://alvinalexander.com/unix/edu/examples/find.shtml

Pipe ( | )

The pipe command, |, takes the output of one command and passes it to another. For example we could “pipe” the output of cat to grep in order to search a file for a particular string

-bash-4.2$ head -5 numbers.txt | grep 1
01
-bash-4.2$ 

history

Displays the command history list with line numbers. You can add an optional integer, n, argument to display only the last n commands

-bash-4.2$ history 2
  299  cat numbers.txt | grep 1
  300  history 2
-bash-4.2$ 

Note: history, |, and grep when used together are a powerful combination as they allow you to search for old commands that you may not remember the exact syntax for:

-bash-4.2$ history | grep chmod
  153  chmod u+x myscript.sh 
  204  chmod +x myexecutable.sh 
  271  chmod +x myscript.sh 
  273  chmod -x myscript.sh 
  301  history | grep chmod
-bash-4.2$ 

chmod

The chmod commands allow a user to modify the permissions of files and directories that they own. To see the permissions of a file/directory we can use the ls -l command

-bash-4.2$ ls -l
total 4
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 a.out
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 helloworld.c
-rw-r--r-- 1 wsuNID workshop    0 Aug 19 07:15 myscript.sh
drwxr-xr-x 2 wsuNID workshop 4096 Aug 18 21:37 NextDirectoryDown
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile01.txt
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile02.txt
-bash-4.2$

The ten left most characters describe your permissions. The first character describes the file type (- for a file, d for a directory). The next three describe the permissions for the user who owns the file, the middle three describe the permissions for the group that owns the file, and the last three describe the permissions for “others”. The “r” denotes permission to read, the “w” means permission to write, and the “x” indicates permission to execute the file/directory.

The change mode or chmod command allows us to alter those permissions. In the past one had to remember (or google) numeric codes that corresponded to permission states, but modern syntax allows for the addition and subtraction of permissions with greater ease. Now one needs only indicate whose permissions to change and what changes to make. For example, let’s add executable permissions for the user to the file myscript.sh

-bash-4.2$ chmod u+x myscript.sh 
-bash-4.2$ ls -l
total 4
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 a.out
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 helloworld.c
-rwxr--r-- 1 wsuNID workshop    0 Aug 19 07:15 myscript.sh
drwxr-xr-x 2 wsuNID workshop 4096 Aug 18 21:37 NextDirectoryDown
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile01.txt
-rw-r--r-- 1 wsuNID workshop    0 Aug 18 21:50 textfile02.txt

The user (and only the user) can now run the script myscript.sh as an executable. For a more complete introduction see http://alvinalexander.com/linux-unix/linux-chmod-command-permissions-file-directories