Moving around and looking at things
OverviewTeaching: 15 min
Exercises: 5 minQuestions
How do I navigate and look around the system?Objectives
Learn how to navigate around directories and look at their contents
Explain the difference between a file and a directory.
Translate an absolute path into a relative path and vice versa.
Identify the actual command, flags, and filenames in a command-line call.
Demonstrate the use of tab completion, and explain its advantages.
At this point in the lesson, we’ve just logged into the system. Nothing has happened yet, and we’re not going to be able to do anything until we learn a few basic commands. By the end of this lesson, you will know how to “move around” the system and look at what’s there.
Right now, all we see is something that looks like this:
The dollar sign is a prompt, which shows us that the shell is waiting for input; your shell may use a different character as a prompt and may add information before the prompt. When typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it.
Type the command
whoami, then press the Enter key (sometimes marked Return)
to send the command to the shell. The command’s output is the ID of the current
user, i.e., it shows us who the shell thinks we are:
More specifically, when we type
whoami the shell:
- finds a program called
- runs that program,
- displays that program’s output, then
- displays a new prompt to tell us that it’s ready for more commands.
Next, let’s find out where we are by running a command called
stands for “print working directory”). (“Directory” is another word for
“folder”). At any moment, our current working directory (where we are) is
the directory that the computer assumes we want to run commands in unless we
explicitly specify something else. Here, the computer’s response is
/home/yourUsername, which is
directory. Note that the location of your home directory may differ from
system to system.
So, we know where we are. How do we look and see what’s in our current directory?
ls prints the names of the files and directories in the current directory in
alphabetical order, arranged neatly into columns.
Differences between remote and local system
Open a second terminal window on your local computer and run the
lscommand without logging in remotely. What differences do you see?
You would likely see something more like this:
Applications Documents Library Music Public Desktop Downloads Movies Pictures
In addition you should also note that the preamble before the prompt (
$) is different. This is very important for making sure you know what system you are issuing commands on when in the shell.
If nothing shows up when you run
ls, it means that nothing’s there. Let’s
make a directory for us to play with.
mkdir <new directory name> makes a new directory with that name in your
current location. Notice that this command required two pieces of input: the
actual name of the command (
mkdir) and an argument that specifies the name of
the directory you wish to create.
$ mkdir documents
ls again. What do we see?
Our folder is there, awesome. What if we wanted to go inside it and do stuff
there? We will use the
cd (change directory) command to move around. Let’s
cd into our new documents folder.
$ cd documents $ pwd
What is the
~ character? When using the shell,
~ is a shortcut that
Now that we know how to use
cd, we can go anywhere. That’s a lot of
responsibility. What happens if we get “lost” and want to get back to where we
To go back to your home directory, the following three commands will work:
$ cd /home/yourUserName $ cd ~ $ cd
A quick note on the structure of a UNIX (Linux/Mac/Android/Solaris/etc)
filesystem. Directories and absolute paths (i.e. exact position in the system)
are always prefixed with a
/ by itself is the “root” or base directory.
Let’s go there now, look around, and then return to our home directory.
$ cd / $ ls $ cd ~
bin dev initrd local mnt proc root scratch tmp work boot etc lib localscratch nix project run srv usr cvmfs home lib64 media opt ram sbin sys var
The “home” directory is the one where we generally want to keep all of our files. Other folders on a UNIX OS contain system files, and get modified and changed as you install new software or upgrade your OS.
Using HPC filesystems
On HPC systems, you have a number of places where you can store your files. These differ in both the amount of space allocated and whether or not they are backed up.
File storage locations:
- Network filesystem - Your home directory is an example of a network filesystem. Data stored here is available throughout the HPC system and files stored here are often backed up (but check your local configuration to be sure!). Files stored here are typically slower to access, the data is actually stored on another computer and is being transmitted and made available over the network!
- Scratch - Some systems may offer “scratch” space. Scratch space is typically faster to use than your home directory or network filesystem, but is not usually backed up, and should not be used for long term storage.
- Work file system - As an alternative to (or sometimes as well as) Scratch space, some HPC systems offer fast file system access as a work file system. Typically, this will have higher performance than your home directory or network file system and may not be backed up. It differs from scratch space in that files in a work file system are not automatically deleted for you, you must manage the space yourself.
- Local scratch (job only) - Some systems may offer local scratch space while executing a job. (A job is a program which you submit to run on an HPC system, and will be covered later.) Such storage is very fast, but will be deleted at the end of your job.
- Ramdisk (job only) - Some systems may let you store files in a “RAM disk” while running a job, where files are stored directly in the computer’s memory. This extremely fast, but files stored here will count against your job’s memory usage and be deleted at the end of your job.
There are several other useful shortcuts you should be aware of.
.represents your current directory
..represents the “parent” directory of your current location
- While typing nearly anything, you can have bash try to autocomplete what
you are typing by pressing the
Let’s try these out now:
$ cd ./documents $ pwd $ cd .. $ pwd
Many commands also have multiple behaviours that you can invoke with command line ‘flags.’ What is a flag? It’s generally just your command followed by a ‘-‘ and the name of the flag (sometimes it’s ‘–’ followed by the name of the flag). You follow the flag(s) with any additional arguments you might need.
We’re going to demonstrate a couple of these “flags” using
Show hidden files with
-a. Hidden files are files that begin with
files will not appear otherwise, but that doesn’t mean they aren’t there!
“Hidden” files are not hidden for security purposes, they are usually just
config files and other tempfiles that the user doesn’t necessarily need to see
all the time.
$ ls -a
. .. .bash_logout .bash_profile .bashrc documents .emacs .mozilla .ssh
Notice how both
.. are visible as hidden files. Show files, their
size in bytes, date last modified, permissions, and other things with
$ ls -l
drwxr-xr-x 2 yourUsername tc001 4096 Jan 14 17:31 documents
This is a lot of information to take in at once, but we will explain this
ls -l is extremely useful, and tells you almost everything you need
to know about your files without actually looking at them.
We can also use multiple flags at the same time!
$ ls -l -a
[yourUsername@gra-login1 ~]$ ls -la total 36 drwx--S--- 5 yourUsername tc001 4096 Nov 28 09:58 . drwxr-x--- 3 root tc001 4096 Nov 28 09:40 .. -rw-r--r-- 1 yourUsername tc001 18 Dec 6 2016 .bash_logout -rw-r--r-- 1 yourUsername tc001 193 Dec 6 2016 .bash_profile -rw-r--r-- 1 yourUsername tc001 231 Dec 6 2016 .bashrc drwxr-sr-x 2 yourUsername tc001 4096 Nov 28 09:58 documents -rw-r--r-- 1 yourUsername tc001 334 Mar 3 2017 .emacs drwxr-xr-x 4 yourUsername tc001 4096 Aug 2 2016 .mozilla drwx--S--- 2 yourUsername tc001 4096 Nov 28 09:58 .ssh
Flags generally precede any arguments passed to a UNIX command.
takes an extra argument that specifies a directory to look into. When you use
flags and arguments together, the syntax (how it’s supposed to be typed)
generally looks something like this:
$ command <flags/options> <arguments>
ls -l -a on a different directory than the one we’re in would look
$ ls -l -a ~/documents
drwxr-sr-x 2 yourUsername tc001 4096 Nov 28 09:58 . drwx--S--- 5 yourUsername tc001 4096 Nov 28 09:58 ..
Where to go for help?
How did I know about the
-a options? Is there a manual we can look
at for help when we need help? There is a very helpful manual for most UNIX
man (if you’ve ever heard of a “man page” for something, this is
what it is).
$ man ls
LS(1) User Commands LS(1) NAME ls - list directory contents SYNOPSIS ls [OPTION]... [FILE]... DESCRIPTION List information about the FILEs (the current directory by default). Sort entries alphabetically if none of -cftuvSUX nor --sort is specified. Mandatory arguments to long options are mandatory for short options too.
To navigate through the
man pages, you may use the up and down arrow keys to
move line-by-line, or try the spacebar and “b” keys to skip up and down by full
page. Quit the
man pages by typing “q”.
Alternatively, most commands you run will have a
--help option that displays
addition information For instance, with
$ ls --help
Usage: ls [OPTION]... [FILE]... List information about the FILEs (the current directory by default). Sort entries alphabetically if none of -cftuvSUX nor --sort is specified. Mandatory arguments to long options are mandatory for short options too. -a, --all do not ignore entries starting with . -A, --almost-all do not list implied . and .. --author with -l, print the author of each file -b, --escape print C-style escapes for nongraphic characters --block-size=SIZE scale sizes by SIZE before printing them; e.g., '--block-size=M' prints sizes in units of 1,048,576 bytes; see SIZE format below -B, --ignore-backups do not list implied entries ending with ~ # further output omitted for clarity
Unsupported command-line options
If you try to use an option that is not supported,
lsand other programs will print an error message similar to this:
[remote]$ ls -j
ls: invalid option -- 'j' Try 'ls --help' for more information.
Looking at documentation
Looking at the man page for
ls --help, what does the
--human-readable) option do?
Absolute vs Relative Paths
/Users/amanda/data/, which of the following commands could Amanda use to navigate to her home directory, which is
.stands for the current directory.
/stands for the root directory.
- No: Amanda’s home directory is
- No: this goes up two levels, i.e. ends in
~stands for the user’s home directory, in this case
- No: this would navigate into a directory
homein the current directory if it exists.
- Yes: unnecessarily complicated, but correct.
- Yes: shortcut to go back to the user’s home directory.
- Yes: goes up one level.
Relative Path Resolution
Using the filesystem diagram below, if
/Users/thing, what will
ls -F ../backupdisplay?
../backup: No such file or directory
2012-12-01 2013-01-08 2013-01-27
2012-12-01/ 2013-01-08/ 2013-01-27/
original/ pnas_final/ pnas_sub/
- No: there is a directory
- No: this is the content of
Users/thing/backup, but with
..we asked for one level further up.
- No: see previous explanation.
Assuming a directory structure as in the above Figure (File System for Challenge Questions), if
lsto display things in reverse order, what command will display:
pnas_sub/ pnas_final/ original/
ls -r -F
ls -r -F /Users/backup
- Either #2 or #3 above, but not #1.
pwdis not the name of a directory.
lswithout directory argument lists files and directories in the current directory.
- Yes: uses the absolute path explicitly.
- Correct: see explanations above.
What does the command
lsdo when used with the
Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.
lsuse a long listing format, showing not only the file/directory names but also additional information such as the file size and the time of its last modification. The
-hargument makes the file size “human readable”, i.e. display something like
Listing Recursively and By Time
ls -Rlists the contents of directories recursively, i.e., lists their sub-directories, sub-sub-directories, and so on in alphabetical order at each level. The command
ls -tlists things by time of last change, with most recently changed files or directories first. In what order does
ls -R -tdisplay things? Hint:
ls -luses a long listing format to view timestamps.
The directories are listed alphabetical at each level, the files/directories in each directory are sorted by time of last change.
Your current directory is referred to as the working directory.
To change directories, use
To view files, use
You can view help for a command with
tabto autocomplete whatever you’re currently typing.