Command Line Interface¶

The interaction with a HPC cluster happens most of the time using a Command Line Interface (CLI). One the cluster all your interaction is controlled by a program called a shell. You identify that you are in shell when you see what is called a prompt, a set of characters that indicate that the shell is ready to receive instructions to operate.

To issue a command to the shell you type a command, eventually followed for a few arguments. When you end typing the full command you type the ENTER key, the command is executed and if the command is programmed to produce screen output it will appear on your terminal as it executes. Once the command is terminated you get a new prompt indicating that the shell is ready for new commands.

The CLI interface is a powerful way to interact with a remote computer.

It takes little resources on the remote machine allowing the machine to serve tens, hundreds and in some cases even thousands of concurrent users.
The shell is far more than command reader and executioner, it is actually a complete programming language. You can create complex sets of instructions by doing what is called Shell Programming actually the ability to do shell programming is what we use in this document to differentiate a basic user from an advanced user.
Despite of the learning curve being steeper, the CLI give you far more control on the machine, so as you become more comfortable using it you will be able to do things than on a Graphical User Interface are simply cumbersome.

Using a CLI is probably the biggest obstacle than beginners has to overcome before start taking advantage of a HPC cluster. Here we will offer a short straight to the point introduction to the bare minimals of managing files and folders on the shell.

Files and Folders¶

Operating Systems from UNIX legacy, Linux and MacOS being the most prominent examples, uses the idea of folders and files to organize the data on their storage device. Differently from Windows, on UNIX there is not such idea of Drives C: or D: or letters for CD Drives or USB Keys. In UNIX every piece of data on any storage device is logically located in some place of a filesystem tree. Thing about the filesystem tree where the lowest level is called the root folder and is indicated by /. From / you will see branches like /bin, /lib and many others, those are folders. Inside each folder there are potentially more folders and files. The tree structure as a metaphor for storing data is very powerful and in the case of UNIX system that data structure is deeply exploited in UNIX systems, even hardware devices such as sound outputs, hard drives receive a file-like entry on the rooted tree. When you insert a USB drive, Modern Linux distributions and MacOS will mount it automatically, meaning that it will receive a location on the tree, in the case of Linux, the mounting point is usually somewhere inside /media/, in MacOS the mounting point is /Volumes.

In the particular case of your interaction with the HPC cluster there are two important folders that you should be aware of. They are so important that they receive special variables to tell you what they are.

The echo and cat commands¶

Your fist command will show you what those locations are. Execute:

$> echo $HOME
/users/<username>
$> echo $SCRATCH
/scratch/<username>

The first command to learn is echo. The command above uses echo to show the contents of two shell variables $HOME and $SCRATCH. Shell variables are ways to store information in such a way that the shell can use it when needed. Each user on the cluster receives appropriated values for those variables.

Lets explore a bit more the usage of echo. Enter this command line and execute ENTER:

$> echo "I am learning UNIX Commands"
I am learning UNIX Commands

The shell is actually able to do basic arithmetical operations, execute this command:

$> echo $((23+45*2))
113

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))
42

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 exists 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.

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 so the name of the command.

You can even use a nice trick to write small text on a file. Execute the following command, followed by the text that you want to write, sat the end execute Ctrl-D (^D), the Control Key followed by the D key. I am annotating below the location where ^D should be executed:

$> cat > report.log
I am learning UNIX Commands^D
$> cat report.log
I am learning UNIX Commands

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 t first by the large number of existing commands, but in fact most of the time you will be using a very little number of them. Learning those will speed up your learning curve.

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

$> date
Mon Nov  5 12:05:58 EST 2018

Folder commands¶

As we mention 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 important amount of data, exploring several parameters or physical conditions. Organize properly all the data in meaningful folders is very important to research endeavors.

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

The next command is cd. This command is used to change directory. Directory is another name for folder. The term directory is also widely used. At least in UNIX the terms directory and folder are exchangeable. 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 not 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 an 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 on your $SCRATCH folder. This is a good opportunity to start creating one folder there and change your location inside, execute:

$> mkdir test_folder
$> cd test_folder

We have use two new commands here, mkdir allow you to create folders in places where you are authorized to do so. For example 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 working directory (CWD), 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 a error message will be shown on your screen.

The name of the folder is test_folder, notice the underscore between test and folder. In UNIX, there is no restriction having files or directories with spaces but using them 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 consider those spaces as separators for several arguments in your command. Try executing the following:

$> mkdir another folder with spaces
$> ls
another  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 error message will be displayed.

After deleting those folders created by mistake, lets 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
another folder with spaces
test_folder
test folder with spaces

Commands for copy and move¶

The next two commands are cp and mv. They are use 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 destination.

Before doing a few examples with cp and mv lets use a very handy command to create files. The command touch is use 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 demonstrate 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, see 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 mention 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 allow you to delete one or more files entered as arguments. Lets 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. Even if deleting a file is not actually filling with zeros the location of the data, on HPC systems the recovery of data is practice unfeasible. Lets delete the folder even recursively:

$> rm -r even

Summary of Basic Commands¶

The purpose of this brief tutorial is 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.

WVU’s High Performance Computer (HPC) Clusters¶
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`
`pwd`	thorny.hpc.wvu.edu	To be deployed by the end of 2018
`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 directory	`mv old_name new_name`
`rm`	Remove one or more files from the file system tree.	`rm trash_file`