Command Line Interface

Overview

Teaching: 35 min
Exercises: 5 min

Topics

How do I use the Linux terminal?

Objectives

Commands to connect to the HPC

Navigating the filesystem

Creating, moving, and removing files/directories

Command Line Interface

At a high level, a HPC cluster is a big computer to be used by several users at the same time. The users expect to run a variety of scientific codes, store the data needed as input or generated as output. In HPC, compute nodes can communicate with each other efficiently for tasks that are too big for a single computer.

Our interactions with normal computers happen in many different ways, including through a keyboard and mouse, touch screen interfaces, or using speech recognition systems. However in HPC we need an efficient and still very light way of communicating with the computer that acts as the front door of the cluster, the head node. For this, we make use of the shell instead of a graphical user interface (GUI).

The GUI is widely used to interact with personal computers. In the GUI, we give instructions using a keyboard, mouse or touchscreen. This way of interacting with a computer is intuitive and very easy to learn but scales very poorly for large streams of instructions even if they are similar or identical. We recognized that GUIs are useful under some circumstances. Later on in this lesson we will show how to use Open On-demand, a web service that allow you to run interactive executions on the cluster using a web interface and your own browser. For most of this lesson we will use the Command Line Interface and it is important for you to familiarize with it.

For example, you need to copy the third line of each of a thousand text files stored in thousand different folders and paste it into a single file line by line. Using the traditional GUI approach of mouse clicks will take several hours to do this.

This is where we take advantage of the shell - a command-line interface (CLI) to make such repetitive tasks with less effort. It can take a single instruction and repeat it as is or with some modification as many times as we want. The task in the example above can be accomplished in a single line of a few instructions.

The heart of a command-line interface is a read-evaluate-print loop (REPL) so called because when you type a command and press Return (also known as Enter) the shell reads your command, evaluates (or “executes”) it, prints the output of your command, loops back and waits for you to enter another command. The REPL is essential on how we interact with HPC clusters.

Even if you are using a GUI frontend such as Jupyter or RStudio, REPL is there for us to give instructions to computers on what to do next.

The Shell

The Shell is a program which runs other programs rather than doing calculations itself. Those programs can be as complicated as climate modeling software and as simple as a program that creates a new directory. The simple programs which are used to perform stand alone tasks are usually referred to as commands. The most popular Unix shell is Bash, (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

The shell typically uses $ as the prompt, but may use a different symbol like $>.

The prompt

When typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it.
$> ls -al

Why use the Command Line Interface?

Before the usage of Command Line Interface (CLI), computer interaction took place with perforated cards or even switching cables on a big console. Despite all the years of new technology and innovation, the CLI remains one of the most powerful and flexible tools for interacting with computers.

Because it is radically different from a GUI, the CLI can take some effort and time to learn. A GUI presents you with choices for you to click on. With a CLI, the choices are combinations of commands and parameters, more akin to words in a language than buttons on a screen. Because the options not presented to you, some vocabulary is necessary in this new “language”. But a small number of commands gets you a long way, and we’ll cover those essential commands below.

Flexibility and automation

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows and allowing you to repeat them easily.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

The `echo` and `cat` commands

The echo command is very basic; it returns what you give it back to the terminal, kinda like an echo. Execute the command below.

$ echo "I am learning UNIX Commands"

I am learning UNIX Commands

This may not seem that useful right now. However, echo will also print the contents of variable to the terminal. There are some default variables set for each user on the HPCs: $HOME is the pathway to the user’s “home” directory, and $SCRATCH is Similarly the pathway to the user’s “scratch” directory. More info on what those directories are for later, but for now, we can print them to the terminal using the echo command.

$ echo $HOME

/users/<username>

$ echo $SCRATCH

/scratch/<username>

In addition, the shell is able to do basic arithmetical operations, execute this command:

$ echo $((23+45*2))

Notice that as customary in mathematics products take precedence over addition. That is called the PEMDAS order of operations, ie "Parentheses, Exponents, Multiplication and Division, and Addition and Subtraction". Check your understanding of the PEMDAS rule with this command:

$ echo $(((1+2**3*(4+5)-7)/2+9))

Notice that the exponential operation is expressed with the ** operator. The usage of echo is important, otherwise, if you execute the command without echo the shell will do the operation and will try to execute a command called 42 that does not exist on the system. Try by yourself:

$ $(((1+2**3*(4+5)-7)/2+9))

-bash: 42: command not found

As you have seen before, when you execute a command on the terminal in most cases you see the output printed on the screen. The next thing to learn is how to redirect the output of a command into a file. This will be very important later to submit jobs and control where and how the output is produced. Execute the following command:

$ echo "I am learning UNIX Commands" > report.log

With the character > redirects the output from echo into a file called report.log. No output is printed on the screen. If the file does not exist it will be created. If the file exists previously, the file is erased and only the new contents are stored. In fact, > can be used to redirect the output of any command to a file!

To check that the file actually contains the line produced by echo, execute:

$ cat report.log

I am learning UNIX Commands

The cat (concatenate) command displays the contents of one or several files. In the case of multiple files the files are printed in the order they are described in the command line, concatenating the output as per the name of the command.

In fact, there are hundreds of commands, most of them with a variety of options that change the behavior of the original command. You can feel bewildered at first by a large number of existing commands, but in fact most of the time you will be using a very small number of them. Learning those will speed up your learning curve.

Folder commands

As we mentioned before, UNIX organizes data in storage devices as a tree. The commands pwd, cd and mkdir will allow you to know where you are, move your location on the tree, and create new folders. Later we will see how to move folders from one location on the tree to another.

The first command is pwd. Just execute the command on the terminal:

$ pwd

/users/<username>

It is very important at all times to know where in the tree you are. Doing research usually involves dealing with a large amount of data, exploring several parameters or physical conditions. Therefore, organizing the filesystem is absolutely key.

When you log into a cluster, by default you are located on your $HOME folder. That is why the pwd command should return that location in the first instance.

The next command cd is used to change directory. A directory is another name for folder and is widely used; in UNIX, the terms are interchangeable. Other Desktop Operating Systems like Windows and MacOS have the concept of smart folders or virtual folders, where the folder that you see on screen has no correlation with a directory in the filesystem. In those cases the distinction is relevant.

There is another important folder defined in our clusters, its called the scratch folder and each user has its own. The location of the folder is stored in the variable $SCRATCH. Notice that this is internal convection and is not observed in other HPC clusters.

Use the next command to go to that folder:

$ cd $SCRATCH
$ pwd

/scratch/<username>

Notice that the location is different now, if you are using this account for the first time you will not have files on this folder. It is time to learn another command to list the contents of a folder, execute:

$ ls

Assuming that you are using your HPC account for the first time, you will not have anything in your $SCRATCH folder and should therefore see no output from ls. This is a good opportunity to start your filesystem by creating one folder and moving into it, execute:

$ mkdir test_folder
$ cd test_folder

mkdir allows you to create folders in places where you are authorized to do so, such as your $HOME and $SCRATCH folders. Try this command:

$ mkdir /test_folder

mkdir: cannot create directory `/test_folder': Permission denied

There is an important difference between test_folder and /test_folder. The former is a location in your current directory, the later is a location starting on the root directory /. A normal user has no rights to create folders on that directory so mkdir will fail and an error message will be shown on your screen.

Notice that we named it test_folder instead of test folder. In UNIX, there is no restriction regarding files or directories with spaces, but using them can become a nuisance on the command line. If you want to create the folder with spaces from the command line, here are the options:

$ mkdir "test folder with spaces"
$ mkdir another\ test\ folder\ with\ spaces

In any case, you have to type extra characters to prevent the command line application of considering those spaces as separators for several arguments in your command. Try executing the following:

$ mkdir another folder with spaces
$ ls

another folder with spaces  folder  spaces  test_folder  test folder with spaces  with

Maybe is not clear what is happening here. There is an option for ls that present the contents of a directory:

$ ls -l

total 0
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:44 another
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 another folder with spaces
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:44 folder
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:44 spaces
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 test_folder
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 test folder with spaces
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:44 with

It should be clear, now what happens when the spaces are not contained in quotes "test folder with spaces" or escaped as another\ folder\ with\ spaces. This is the perfect opportunity to learn how to delete empty folders. Execute:

$ rmdir another
$ rmdir folder spaces with

You can delete one or several folders, but all those folders must be empty. If those folders contain files or more folders, the command will fail and an error message will be displayed.

After deleting those folders created by mistake, let's check the contents of the current directory. The command ls -1 will list the contents of a file one per line, something very convenient for future scripting:

$ ls -1

total 0
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 another folder with spaces
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 test_folder
drwxr-xr-x 2 myname mygroup 512 Nov  2 15:45 test folder with spaces

Commands for copy and move

The next two commands are cp and mv. They are used to copy or move files or folders from one location to another. In its simplest usage, those two commands take two arguments, the first argument is the source and the last one the destination. In the case of more than two arguments, the destination must be a directory. The effect will be to copy or move all the source items into the folder indicated as the destination.

Before doing a few examples with cp and mv, let's use a very handy command to create files. The command touch is used to update the access and modification times of a file or folder to the current time. In case there is not such a file, the command will create a new empty file. We will use that feature to create some empty files for the purpose of demonstrating how to use cp and mv.

Lets create a few files and directories:

$ mkdir even odd
$ touch f01 f02 f03 f05 f07 f11

Now, lets copy some of those existing files to complete all the numbers up to f11:

$ cp f03 f04
$ cp f05 f06
$ cp f07 f08
$ cp f07 f09
$ cp f07 f10

This is good opportunity to present the * wildcard, use it to replace an arbitrary sequence of characters. For instance, execute this command to list all the files created above:

$ ls f*

f01  f02  f03  f04  f05  f06  f07  f08  f09  f10  f11

The wildcard is able to replace zero or more arbitrary characters, for example:

$ ls f*1

f01  f11

There is another way of representing files or directories that follow a pattern, execute this command:

$ ls f0[3,5,7]

f03  f05  f07

The files selected are those whose last character is on the list [3,5,7]. Similarly, a range of characters can be represented. See:

$ ls f0[3-7]

f03  f04  f05  f06  f07

We will use those special character to move files based on its parity. Execute:

$ mv f[0,1][1,3,5,7,9] odd
$ mv f[0,1][0,2,4,6,8] even

The command above is equivalent to execute the explicit listing of sources:

$ mv f01 f03 f05 f07 f09 f11 odd
$ mv f02 f04 f06 f08 f10 even

Delete files and Folders

As we mentioned above, empty folders can be deleted with the command rmdir but that only works if there are no subfolders or files inside the folder that you want to delete. See for example what happens if you try to delete the folder called odd:

$ rmdir odd

rmdir: failed to remove `odd': Directory not empty

If you want to delete odd, you can do it in two ways. The command rm allows you to delete one or more files entered as arguments. Let's delete all the files inside odd, followed by the deletion of the folder odd itself:

$ rm odd/*
$ rmdir odd

Another option is to delete a folder recursively, this is a powerful but also dangerous option. Quite unlike Windows/MacOS, recovering deleted files through a “Trash Can” or “Recycling Bin” does not happen in Linux; deleting is permanent. Let's delete the folder even recursively:

$ rm -r even

Summary of Basic Commands

The purpose of this brief tutorial is to familiarize you with the most common commands used in UNIX environments. We have shown 10 commands that you will be using, very often on your interaction. This 10 basic commands and one editor from the next section is all that you need to be ready for submitting jobs on the cluster.

The next table summarizes those commands.

Command	Description	Examples
`echo`	Display a given message on the screen	`$ echo "This is a message"`
`cat`	Display the contents of a file on screen Concatenate files	`$ cat my_file`
`date`	Shows the current date on screen	`$ date` Sun Jul 26 15:41:03 EDT 2020
`pwd`	Return the path to the current working directory	`$ pwd` /users/username
`cd`	Change directory	`$ cd sub_folder`
`mkdir`	Create directory	`$ mkdir new_folder`
`touch`	Change the access and modification time of a file Create empty files	`$ touch new_file`
`cp`	Copy a file in another location Copy several files into a destination directory	`$ cp old_file new_file`
`mv`	Move a file in another location Move several files into a destination folder	`$ mv old_name new_name`
`rm`	Remove one or more files from the file system tree	`$ rm trash_file` `$ rm -r full_folder`

Exercise 1

Get into Thorny Flat with your training account and execute the commands ls, date and cal

Exit from the cluster with exit

So let’s try our first command, which will list the contents of the current directory:
[training001@srih0001 ~]$ ls -al
total 64
drwx------   4 training001 training   512 Jun 27 13:24 .
drwxr-xr-x 151 root        root     32768 Jun 27 13:18 ..
-rw-r--r--   1 training001 training    18 Feb 15  2017 .bash_logout
-rw-r--r--   1 training001 training   176 Feb 15  2017 .bash_profile
-rw-r--r--   1 training001 training   124 Feb 15  2017 .bashrc
-rw-r--r--   1 training001 training   171 Jan 22  2018 .kshrc
drwxr-xr-x   4 training001 training   512 Apr 15  2014 .mozilla
drwx------   2 training001 training   512 Jun 27 13:24 .ssh
Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:
$ ks
ks: command not found
Usually this means that you have mis-typed the command.

Exercise 2

Commands in Unix/Linux are very stable with some existing for decades now. This exercise begins to give you a feeling of the different parts of a command.

Execute the command cal, we executed the command before but this time execute it again like this cal -y. You should get an output like this:

[training001@srih0001 ~]$ cal -y

                         2021

January               February                 March
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa
1  2       1  2  3  4  5  6       1  2  3  4  5  6
3  4  5  6  7  8  9    7  8  9 10 11 12 13    7  8  9 10 11 12 13
10 11 12 13 14 15 16   14 15 16 17 18 19 20   14 15 16 17 18 19 20
17 18 19 20 21 22 23   21 22 23 24 25 26 27   21 22 23 24 25 26 27
24 25 26 27 28 29 30   28                     28 29 30 31
31
April                   May                   June
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa
1  2  3                      1          1  2  3  4  5
4  5  6  7  8  9 10    2  3  4  5  6  7  8    6  7  8  9 10 11 12
11 12 13 14 15 16 17    9 10 11 12 13 14 15   13 14 15 16 17 18 19
18 19 20 21 22 23 24   16 17 18 19 20 21 22   20 21 22 23 24 25 26
25 26 27 28 29 30      23 24 25 26 27 28 29   27 28 29 30
30 31
July                  August                September
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa
1  2  3    1  2  3  4  5  6  7             1  2  3  4
4  5  6  7  8  9 10    8  9 10 11 12 13 14    5  6  7  8  9 10 11
11 12 13 14 15 16 17   15 16 17 18 19 20 21   12 13 14 15 16 17 18
18 19 20 21 22 23 24   22 23 24 25 26 27 28   19 20 21 22 23 24 25
25 26 27 28 29 30 31   29 30 31               26 27 28 29 30

October               November               December
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa
1  2       1  2  3  4  5  6             1  2  3  4
3  4  5  6  7  8  9    7  8  9 10 11 12 13    5  6  7  8  9 10 11
10 11 12 13 14 15 16   14 15 16 17 18 19 20   12 13 14 15 16 17 18
17 18 19 20 21 22 23   21 22 23 24 25 26 27   19 20 21 22 23 24 25
24 25 26 27 28 29 30   28 29 30               26 27 28 29 30 31
31

Another very simple command that is very useful in HPC is date. Without any arguments, it prints the current date to the screen.

$ date

Sun Jul 26 15:41:03 EDT 2020

Exercise 3

Create two folders called one and two. In one create the empty file none1 and in two create > the empty file none2.

Create also in those two folders, files date1 and > date2 by redirecting the output from the command date > using >.
$ date > date1
Check with cat that those files contain dates.

Now, create the folders empty_files and dates and move > the corresponding files none1 and none2 to > empty_files and do the same for date1 and date2.

The folders one and two should be empty now; delete > them with rmdir Do the same with folders empty_files and dates with rm -r.

Exercise 4

The command line is powerful enough to allow you to even do programming. Execute the command below and see the answer.
[training001@srih0001 ~]$ n=1; while test $n -lt 10000; do  echo $n; n=`expr 2 \* $n`; done
1
2
4
8
16
32
64
128
256
512
1024
2048
4096
8192
If you are not getting this output check the command line very carefully. Even small changes could be interpreted by the shell as entirely different commands so you need to be extra careful and gather insight when commands are not doing what you want.

Now the challenge consists on tweaking the command line above to show the calendar for August for the next 10 years.

Hint

Use the command cal -h to get a summary of the arguments to show just one month for one specific year You can use expr to increase n by one on each cycle, but you can also use n=$(n+1)

Grabbing files from the internet

To download files from the internet, the absolute best tool is wget. The syntax is relatively straightforwards: wget https://some/link/to/a/file.tar.gz

Downloading the Drosophila genome

The Drosophila melanogaster reference genome is located at the following website: http://metazoa.ensembl.org/Drosophila_melanogaster/Info/Index. Download it to the cluster with wget.
cd to your genome directory
Copy this url and paste it onto the command line:
$> wget ftp://ftp.ensemblgenomes.org:21/pub/metazoa/release-51/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.32.dna_rm.toplevel.fa.gz

Working with compressed files, using unzip and gunzip

The file we just downloaded is gzipped (has the .gz extension). You can uncompress it with gunzip filename.gz.

File decompression reference:

.tar.gz - tar -xzvf archive-name.tar.gz

.tar.bz2 - tar -xjvf archive-name.tar.bz2

.zip - unzip archive-name.zip

.rar - unrar archive-name.rar

.7z - 7z x archive-name.7z

However, sometimes we will want to compress files ourselves to make file transfers easier. The larger the file, the longer it will take to transfer. Moreover, we can compress a whole bunch of little files into one big file to make it easier on us (no one likes transferring 70000) little files!

The two compression commands we’ll probably want to remember are the following:

Compress a single file with Gzip - gzip filename

Compress a lot of files/folders with Gzip - tar -czvf archive-name.tar.gz folder1 file2 folder3 etc

Key Points

The basic commands you must know are echo, cat, date, pwd, cd, mkdir, touch, cp, mv, rm. You will use these commands very often.

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Command Line Interface

Overview