Part 4 - Files and File Systems

About File Systems 

So far all the files we've been dealing with have been in your Home directory, which is your personal directory. All Unix systems will provide you with a Home directory of your own.

Files and directories in your Home directory are part of the overall file system hierarchy – a tree of directories and their files/sub-directories.

To see the partial file system hierarchy of your Home directory, you can use the tree command. (Note that tree is not always available on Linux systems; it is an add-on tool that must be installed separately).

Just calling tree will produce output similar to this:

This display shows the hierarchical structure of files and sub-directories. At top-level, there are a number of files that we pre-positioned for you (haiku.txt, mobydick.txt, etc.) along with some we created (out.txt, newfile.txt, etc.). There are also two sub-directories: bedfiles and docs, each with several files in them. And notice how tree colors the directories differently to make them stand out.

Of course there are other areas of the file system hierarchy a tree of. For example, the /stor/work/CBRS_unix directory.

tree /stor/work/CBRS_unix

Produces output similar to this:

There are three sub-directories under the /stor/work/CBRS_unix directory: fastq, test and unix, each with their own sub-directories and files. Again, notice how tree colors file with the extension .gz differently. These are FASTQ files, compressed using the gzip protocol, produced by a Next Generation Sequencing (NGS) run in our Genome Sequencing and Analysis (GSAF) core facility.

Note that in Unix, and on Macs, directories are separated by forward slash ( / ) characters, unlike Windows where the backslash ( \ ) is used. And the root of all the file systems is that 1st forward slash.

Finding file systems

So if you're on a new system, how do you know what file systems are available to you? The df (disk free) command will list all the available file systems. As its name suggests, it also shows file system sizes, so it's always good to use df -h (human readable) to see sizes in more readable form. Also, there can be many many file systems available on any given system, so always pipe the output to more.

df -h | more

This produces a rather busy display like this one:

Fortunately, you can ignore most of it. Focus on the Mounted on and Size columns.

• / (forward slash), under the Mounted on column:
  • / (forward slash) is the root of the file system where the operating system is installed
  • Note its Size is 98G with 47G used
• Look for Mounted on entries with large Size numbers:
  • Gigabytes (10^{^9} bytes), Terabytes (10^{^12} bytes), Petabytes (10^{^15} bytes)
• Ignore file systems with names like /run, /dev, /snap, /sys, /boot, /tmp, /var – these are system related
• Here we see a number starting with /stor (/stor, /stor/home, /stor/work, etc.)
  • Note its large Size: 39T - a sign that it's a file system you want to know about.

Here's a similar listing from the Lonestar5 compute cluster at TACC:

Here the big important file systems are /home1 (7.0T), /scratch (8.1P) and /work (6.8P). There's also /admin (3.5T) but its name suggests that normal users won't be able to access it.

Navigating the file system

Now that we know there are other places, how do we get there? Enter the cd (change directory) command:

• cd <optional directory_name>
  • with no argument, always changes to your Home directory.

There are also some "special" built-in directory names:

• ~ (tilde) means my Home directory
• . (single period) means the current directory
• .. (two periods) means the parent of the current directory (directory above it)
  
  • So ls .. means "list contents of the parent directory"
• - (dash) means whatever directory you were in before this one

So these two expressions do the same thing – take you to your Home directory from wherever you are in the file system.

cd
cd ~

When you've changed into a directory, how do you know where you are in the file system?

• On our system, we've arranged that the command prompt "follows you" around the file system.
• On other systems you can use the pwd (present working directory) command to see where you are

Exercise 4-1

Change into the /stor/work/CBRS_unix directory then back to your Home directory. Then use the - (dash) to go back to /stor/work/CBRS_unix without typing it in, then Home again using ~ (tilde). How does the command prompt change?

cd /stor/work/CBRS_unix
cd                          # Back home
cd -                        # Last directory (here /stor/work/CBRS_unix)
cd ~                        # And home again

Tab key completion

The Tab key is your best friend! Hit the Tab key once or twice - it's almost always magic!

Hitting Tab invokes shell completion, instructing the shell to try to guess what you're doing and finish the typing for you. On most modern Linux shells you use Tab completion by pressing:

• single Tab – completes file or directory name up to any ambiguous part
  • if nothing shows up, there is no unambiguous match
• Tab twice – display all possible completions
  
  • you then decide where to go next

Let's have some fun with the Tab key. Follow along if you can:

cd /st                   # hit Tab key - expands to /stor/ which is the only match
cd /stor/w               # hit Tab key again - expands to /stor/work/, again the only match
cd /stor/work/C          # hit Tab once - nothing happens because there are multiple matches
cd /stor/work/C          # hit Tab a 2nd time - all matching directories listed
cd /stor/work/CB         # hit Tab key - expands to /stor/work/CBRS_unix
cd /stor/work/CBRS_unix  # press Enter to change to that directory
cd                       # go Home

Relative pathname syntax

Rather than always typing a full pathname (that is, a pathname starting with the / root directory) of where you want to go, you can specify a directory relative to where you are. This is where the special directory names . (single period =  current directory) and .. (double period =  parent of current directory) come in handy.

Here are some examples. Follow along if you can – and use the Tab key to help out!

pwd                     # where am I now, really? /stor/home/student01
cd ..                   # up one level - now I'm in /stor/home
cd ../work/CBRS_unix/   # change into /stor/work/CBRS_unix using relative syntax
cd ./unix/docs/         # change into the unix/docs sub-directory relative to /stor/work/CBRS_unix
cd ../../fastq/         # go up two levels, then into fastq directory
cd ../../../home/       # change to the /stor/home directory using relative syntax
cd                      # go Home

Pathname wildcards ("globbing")

Since we've seen that a goal of Unix is to type as little as possible, there are several metacharacters that serve as wildcards to represent sets of characters when typing file names. Using these metacharacters is called globbing (don't ask me why ) and the pattern is called a glob.

• asterisk ( * ) is the most common filename wildcard. It matches any length of any characters.
• brackets ( [ ] ) match any character between the brackets.
  • and you can use a hyphen ( - ) to specify a range of characters (e.g. [A-G])
• braces ( {  } ) enclose a list of comma-separated strings to match (e.g. {dog,pony})

And wildcards can be combined. Some examples:

ls *.txt        # lists all files with names ending in ".txt"
ls [a-z]*.txt   # does the same but only lists files starting with a lowercase letter
ls [ABhi]*      # lists all filenames whose 1st letter is A, B, h, or i
ls *.{txt,tsv}  # lists filenames ending in either .txt or .tsv

Exercise 4-2

Design a wildcard that will match the files haiku.txt and mobydick.txt but not jabberwocky.txt in your Home directory.

ls [hm]*.txt
ls {haiku,jabberwocky}.txt 

File attributes

Let's revisit a listing of our Home directory contents. Before we created any files, an ls -l listing looked something like this:

Ignoring that "total 779" line, there are 9 whitespace-separated columns in this long listing:

1. file permissions - a 10-character field
2. number of sub-directories or symbolic links associated with a directory - rarely important
3. account name of the file owner
4. Unix group associated with the file
5. file size
6. last modification month
7. last modification day
8. last modification year, or last modification hour/minute if within the last year
9. file name

Notice I call everything a file, even directories. That's because directories are just a special kind of file – one that contains information about the directory's contents.

Owner and Group

A file's owner is the Unix account that created the file (here student01, me). That account belongs to one or more Unix groups, and the group associated with a file is listed in field 4.

The owner will always be a member of the group associated with a file, and other accounts may also be members of the same group. The Unix group for our class is CCBB_Workshops_1. (To see the Unix groups you belong to, just type the groups command.)

Permissions

File permissions (and some information about the file type) are encoded in that 1st 10-character field. Permissions govern who can access a file, and what actions they are allowed.

• character 1 describes the file type (d for directory, - for regular file, l for symbolic link)
• the remaining 9 characters are 3 sets of 3-character designations
  • characters 2-4: what the owning user account can do
  • characters 5-7: what other members of the associated Unix group can do
  • characters 8-19: what other non-group members (everyone) can do

Each of the 3-character sets describes if read ( r ) write ( w or s ) and execute ( x ) actions are allowed, or not allowed ( - ).

• read ( r ) access means file contents can be read, and it can be copied
• write ( w or s ) access means a file's contents can be changed, and directory contents can be modified (files added or deleted)
• execute ( x )
  • For files, execute ( x ) means it is a program that can be called/executed (e.g. /usr/bin/ls, the file that performs the ls command)
  • For directories, execute ( x ) means directory operations may be performed/executed
    • the directory can be listed and changed into

Examples:

ls -l ~/haiku.txt

ls -l /usr/bin/ls

ls -ld ~/docs (-d says to list directory information, not directory contents)

Exercise 4-3

What are the directory permissions and ownership of /stor/work/CBRS_unix/test? Can you list its contents? Why or why not?

What are the directory permissions and ownership of /stor/work/CBRS_unix/test/anna_only? Can you list its contents? Why or why not?