Navigating the File System

This section is going to be a high-level talk about the Linux filesystem concepts, not a low-level description of filesystem types.

Learning objectives

Questions

  • How do I change directory?
  • How do I list my files?

Learning objectives

  • Learn how to navigate the Linux file system
  • Learn about files and directories
  • Learn about paths
  • Learn about options (flags) and arguments to shell commands
  • Learn about the tab completion

Tree of dir structure

The Linux filesystem directory structure starts with the top root directory, which is shown as /. Below this are several other standard directories. Of particular interest are usr/bin, home, usr/lib, and usr/lib64. A common directory which you will also often find is usr/local/bin.

The picture on the right shows typical subdirectories under / (note that the command ‘tree’ does not work at all HPC centres, though it does work on Tetralith - see the page tree under “Extras section for how to install if it is missing). Some of the directories have a symbolic link to a different name - this is often done to make it quicker to write, but can also be for compatibility reasons since some software have hardcoded paths.

Note

The path or pathname is the representation of the location of a file or folder/directory on a computer file system.

  • / is the root of the directory structure on a Linux filesystem
  • /usr/bin contains (most) of the system-specific binaries
  • /usr/local/bin holds non-system binaries. often locally compiled/maintained packages
  • /home is where the home directories of the users of the system are located
  • /usr/lib holds kernel modules and shared library images needed to boot the system and run commands in the root filesystem
  • /usr/lib64 is the same as /usr/lib, just for 64-bit libraries

User-installed binaries are often located in /opt.

The file system could also be illustrated like this:

folders of filesystem structure

Note

The character / can be

  1. the root directory, if it is at the front of a file or directory name
  2. a separator if it appears inside a path.

Note

If you are on a local cluster, on an HPC centre, etc. where you are not root, you will as default be in your home directory when you login. You can use cd .. a couple times to go to the root of the system and do tree there if you want, or do tree in your home directory (you can always return there with just cd).

Running tree in / on a supercomputing centre will probably give a very large/long output!

Home folders on Tetralith

home folders file structure


The above shows an illustration where the home folders are emphasized.

Your home directory

When you login to the computer (as a non root user), you will end up in your home directory.

The path to your home directory varies somewhat. Here are some examples for me:

  • Tetralith: /home/x_birbr
  • Kebnekaise: /home/b/bbrydsoe
  • My laptop, ncc-1701: /home/bbrydsoe
  • My home desktop, defiant: /home/bbrydsoe

Note

You can always use the command pwd to see the actualy path!

You will always return to your home directory by giving the command cd and pressing enter.

There are is also an “environment variable” that can be used as shortcut for the path: $HOME. We will talk more about (environment) variables later.

pwd

The command pwd (print working directory) will print out the full pathname of the working directory to the screen.

You can use this to find out which directory you are in.

Example, in your home directory

user x_birbr: 

[x_birbr@tetralith3 ~]$ pwd
/home/x_birbr
[x_birbr@tetralith3 ~]$

user bbrydsoe: 

b-an01 [~]$ pwd
/home/b/bbrydsoe
b-an01 [~]$

Example, in a directory named testdir

On Tetralith, user x_birbr:

[x_birbr@tetralith3 testdir]$ pwd
/home/x_birbr/testdir
[x_birbr@tetralith3 testdir]$

Example, in subdirectory mydir under directory testdir

On Tetralith, user x_birbr: 

[x_birbr@tetralith3 mydir]$ pwd
/home/x_birbr/testdir/mydir
[x_birbr@tetralith3 mydir]$

cd - changing directory

The command cd is used to change directory.

  • cd: Go to your home directory ($HOME)
  • cd DIR: Change directory to DIR
  • cd ..: Change directory to the parent directory of the current directory
  • cd -: go back to the previous directory

Example

This is the structure of the exercises directory that you got after extracting the tarball:

folders of exercises directory structure

Remember, $HOME is an environment variable which gives a shortcut to your home directory.

NOTE if you are on Tetralith and placed the exercises under /proj/linux-intro/users/USERNAME then $HOME would be replaced by that path.

To change to the directory exercises when you are in your home directory, you do 

cd exercises

To then change to the directory testdir1 you do 

cd testdir1

To quickly go back to your home directory, do 

cd

To quickly go to a subdirectory, for instance exercises/testdir2 you then do 

cd exercises/testdir2

To go to the above directory from anywhere on the system in question, do 

cd $HOME/exercises/testdir2

Info

You can use full paths (also know as absolute paths) or relative paths to give the location.

An absolute path makes no assumptions about your current location in relation to the location of the file or directory you want to access. It specifies the location from the root of the file system.

The path with reference to your current directory is called the relative path.

ls - listing files/directories

The ls command is used to list files. If you just give the command “ls” with no flags it will list all files in the current directory except for hidden files.

ls [flags] [directory]

This way you can to list files/subdirectories for any directory, but the default one is the one you are currently standing in.

Some examples:

  • ls / lists contents of the root directory
  • ls .. lists the contents of the parent directory of the current
  • ls ~ lists the contents of your user home directory
  • ls * lists contents of current directory and subdirectories

Commonly used flags

  • -d */ lists only directories
  • -a lists content including hidden files and directories
  • -l lists content in long table format (permissions, owners, size in bytes, modification date/time, file/directory name)
  • -lh adds an extra column to above representing size of each file/directory
  • -t lists content sorted by last modified date in descending order
  • -tr lists content sorted by last modified date in ascending order
  • -R lists contents recursively in all subdirectories
  • -s list files with their sizes
  • -S sort files/directories by size in descending order
  • -Sr sort files/directories by size in ascending order

To get more flags, type ls --help or man ls in the terminal to see the manual.

Tip

You can often get more info on flags/options and usage for a Linux command with

  • COMMAND --help
  • man COMMAND

where COMMAND is the Linux command you want information about, like ls, mkdir, etc.

The output for a few of the flags, for a directory with two subdirectories and some files

[x_birbr@tetralith1 mytestdir]$ ls
myfile.txt  myotherfile.txt  testdir1  testdir2

[x_birbr@tetralith1 mytestdir]$ ls -a
./  ../  myfile.txt  myotherfile.dat  testdir1/  testdir2/

[x_birbr@tetralith1 mytestdir]$ ls -l
total 3
-rw-rw-r-- 1 x_birbr x_birbr   27 Sep 11 11:43 myfile.txt
-rw-rw-r-- 1 x_birbr x_birbr   33 Sep 11 11:43 myotherfile.txt
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:40 testdir1
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:39 testdir2

[x_birbr@tetralith1 mytestdir]$ ls -la
total 5
drwxrwxr-x 4 x_birbr x_birbr 4096 Sep 11 11:43 .
drwx------ 3 x_birbr x_birbr 4096 Sep 11 11:43 ..
-rw-rw-r-- 1 x_birbr x_birbr   27 Sep 11 11:43 myfile.txt
-rw-rw-r-- 1 x_birbr x_birbr   33 Sep 11 11:43 myotherfile.txt
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:40 testdir1
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:39 testdir2

[x_birbr@tetralith1 mytestdir]$ ls -lah
total 5.0K
drwxrwxr-x 4 x_birbr x_birbr 4.0K Sep 11 11:43 .
drwx------ 3 x_birbr x_birbr 4.0K Sep 11 11:43 ..
-rw-rw-r-- 1 x_birbr x_birbr   27 Sep 11 11:43 myfile.txt
-rw-rw-r-- 1 x_birbr x_birbr   33 Sep 11 11:43 myotherfile.txt
drwxrwxr-x 2 x_birbr x_birbr 4.0K Sep 11 11:40 testdir1
drwxrwxr-x 2 x_birbr x_birbr 4.0K Sep 11 11:39 testdir2

[x_birbr@tetralith1 mytestdir]$ ls -latr
total 5
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:39 testdir2
drwxrwxr-x 2 x_birbr x_birbr 4096 Sep 11 11:40 testdir1
-rw-rw-r-- 1 x_birbr x_birbr   27 Sep 11 11:43 myfile.txt
-rw-rw-r-- 1 x_birbr x_birbr   33 Sep 11 11:43 myotherfile.txt
drwx------ 3 x_birbr x_birbr 4096 Sep 11 11:43 ..
drwxrwxr-x 4 x_birbr x_birbr 4096 Sep 11 11:43 .

[x_birbr@tetralith1 mytestdir]$ ls *
myfile.txt  myotherfile.dat

testdir1:
file1.txt  file2.sh  file3.c  file4.dat

testdir2:
file1.txt  file2.txt  file3.c

[x_birbr@tetralith1 mytestdir]$ cd testdir1
b-an01 [~/mytestdir/testdir1]$ ls -l
total 2
-rw-rw-r-- 1 x_birbr x_birbr 31 Sep 11 11:47 file1.txt
-rw-rw-r-- 1 x_birbr x_birbr 16 Sep 11 11:49 file2.sh
-rw-rw-r-- 1 x_birbr x_birbr 74 Sep 11 11:49 file3.c
-rw-rw-r-- 1 x_birbr x_birbr 25 Sep 11 11:50 file4.dat

[x_birbr@tetralith1 mytestdir]$ ls -ls
total 2
1 -rw-rw-r-- 1 x_birbr x_birbr 31 Sep 11 11:47 file1.txt
1 -rw-rw-r-- 1 x_birbr x_birbr 16 Sep 11 11:49 file2.sh
1 -rw-rw-r-- 1 x_birbr x_birbr 74 Sep 11 11:49 file3.c
1 -rw-rw-r-- 1 x_birbr x_birbr 25 Sep 11 11:50 file4.dat

The “drwxr-xr-x” and “-rw-r--r--” are examples of permissions. The prefex d means is it a directory. A “-” means no permission for that. There are three groups: owner, group, and all. Note that “r” is for read, “w” is for write, and “x” is for execute.

We will talk a bit more about permissions and how to change them when we come to the section on scripting.

Keypoints

  • Your home directory is generally located in /home/USERNAME or /home/U/USERNAME
  • Your home directory can also be addressed with the environment variable $HOME
  • pwd is useful for determining your path and current location
  • To change directory you use the command cd DIR
  • Just giving the command cd takes you to your homedirectory
  • ls is used to list files and directories