Tutorials

We are providing a collection of tutorials to allow self-paced training on various aspects of using OSC resources. Please contact us if you feel there is a specific tutorial that would be of use to the community.

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UNIX Basics

Linux Command Line Fundamentals

This tutorial teaches you about the linux command line and shows you some useful commands. It also shows you how to get help in linux by using the man and apropos commands.


Batch Tutorial

This tutorial guides you through the process of creating and submitting a batch script on one of our compute clusters. This is a linux tutorial which uses batch scripting as an example, not a tutorial on writing batch scripts. The primary goal is not to teach you about batch scripting, but for you to become familiar with certain linux commands that can be used either in a batch script or at the command line. There are other pages on the OSC web site that go into the details of submitting a job with a batch script.


Tar Tutorial

This tutorial shows you how to download tar (tape archive) files from the internet and how to deal with large directory trees of files.


Managing your environment with .bashrc, .login, and other "dot files" (Coming Soon)

This tutorial explains the purpose of the "dot" files in your home directory and how to fill them with useful things.


Linux Shortcuts

This tutorial shows you some handy time-saving shortcuts in linux. Once you have a good understanding of how the command line works, you will want to learn how to work more efficiently.

Service: 

Linux Command Line Fundamentals

Description

This tutorial teaches you about the linux command line and shows you some useful commands. It also shows you how to get help in linux by using the man and apropos commands.

Prerequisites

None.

Introduction

Unix is an operating system that comes with several application programs. Other examples of operating systems are Microsoft Windows, Apple OS and Google's Android. An operating system is the program running on a computer (or a smartphone) that allows the user to interact with the machine -- to manage files and folders, perform queries and launch applications. In graphical operating systems, like Windows, you interact with the machine mainly with the mouse. You click on icons or make selections from the menus. The Unix that runs on OSC clusters gives you a command line interface. That is, the way you tell the operating system what you want to do is by typing a command at the prompt and hitting return. To create a new folder you type mkdir. To copy a file from one folder to another, you type cp. And to launch an application program, say the editor emacs, you type the name of the application. While this may seem old-fashioned, you will find that once you master some simple concepts and commands you are able to do what you need to do efficiently and that you have enough flexibility to customize the processes that you use on OSC clusters to suit your needs.

Common Tasks on OSC Clusters

What are some common tasks you will perform on OSC clusters? Probably the most common scenario is that you want to run some of the software we have installed on Glenn and Oakley. You may have your own input files that will be processed by an application program. The application may generate output files which you need to organize. You will probably have to create a job script so that you can execute the application in batch mode. To perform these task, you need to develop a few different skills. Another possibility is that you are not just a user of the software installed on Glenn and Oakley but a developer of your own software -- or maybe you are making some modifications to an application program so you need to be able to build the modified version and run it. In this scenario you need many of the same skills plus some others. This tutorial shows you the basics of working with the Unix command line. Other tutorials go into more depth to help you learn more advanced skills.

The Kernel and the Shell

You can think of Unix as consisting of two parts -- the kernel and the shell. The kernel is the guts of the Unix operating system -- the core software running on a machine that performs the infrastructure tasks like making sure multiple users can work at the same time. You don't need to know anything about the kernel for the purposes of this tutorial. The shell is the program that interprets the commands you enter at the command prompt. There are several different flavors of Unix shells -- Bourne, Korn, Cshell, TCshell and Bash. There are some differences in how you do things in the different shells, but they are not major and they shouldn't show up in this tutorial. However, in the interest of simplicity, this tutorial will assume you are using the Bash shell. This is the default shell for OSC users. Unless you do something to change that, you will be running the Bash shell when you log onto Oakley or Glenn.

The Command Prompt

The first thing you need to do is log onto one of the OSC clusters, Oakley or Glenn. If you do not know how to do this, you can find help at the OSC home page. If you are connecting from a Windows system, you need to download and setup the OSC Starter Kit which you can find here. If you are connecting from a Mac or Linux system, you will use ssh. To get more information about using ssh, go to the OSC home page, hold your cursor over the "Supercomputing" menu in the main blue menu bar and select "FAQ." This should help you get started. Once you are logged in look for the last thing displayed in the terminal window. It should be something like

-bash-3.2$

with a block cursor after it. This is the command prompt -- it's where you will see the commands you type in echoed to the screen. In this tutorial, we will abbreviate the command prompt with just the dollar sign - $. The first thing you will want to know is how to log off. You can log off of the cluster by typing "exit" then typing the <Enter> key at the command prompt:

$ exit <Enter>

For the rest of this tutorial, when commands are shown, the <Enter> will be omitted, but you must always enter <Enter> to tell the shell to execute the command you just typed.

First Simple Commands

So let's try typing a few commands at the prompt (remember to type the <Enter> key after the command):

$ date

$ cal

$ finger

$ who

$ whoami

$ finger -l

That last command is finger followed by a space then a minus sign then the lower case L. Is it obvious what these commands do? Shortly you will learn how to get information about what each command does and how you can make it behave in different ways. You should notice the difference between "finger" and "finger -l" -- these two commands seem to do similar things (they give information about the users who are logged in to the system) but they print the information in different formats. try the two commands again and examine the output. Note that you can use the scroll bar on your terminal window to look at text that has scrolled off the screen.

man

The "man" command is how you find out information about what a command does. Type the following command:

$ man

It's kind of a smart-alecky answer you get back, but at least you learn that "man" is short for "manual" and that the purpose is to print the manual page for a command. Before we start looking at manual pages, you need to know something about the way Unix displays them. It does not just print the manual page and return you to the command prompt -- it puts you into a mode where you are interactively viewing the manual page. At the bottom of the page you should see a colon (:) instead of the usual command prompt (-bash-3.2$). You can move around in the man page by typing things at the colon. To exit the man page, you need to type a "q" followed by <Enter>. So try that first. Type

$ man finger

then at the colon of the man page type

: q

You do not have to type <Enter> after the "q" (this is different from the shell prompt.) You should be back at the shell prompt now. Now let's go through the man page a bit. Once again, type

$ man finger

Now instead of just quitting, let's look at the contents of the man page. The entire man page is probably not displayed in your terminal. To scroll up or down, use the arrow keys or the <Page Up> and <Page Down> keys of the keyboard. The <Enter> and <Space> keys also scroll. Remember that "q" will quit out of the man page and get you back to the shell prompt.

The first thing you see is a section with the heading "NAME" which displays the name of the command and a short summary of what it does. Then there is a section called "SYNOPSIS" which shows the syntax of the command. In this case you should see

SYNOPSIS

     finger [-lmsp] [user ...] [user@host ...]

Remember how "finger" and "finger -l" gave different output? The [-lmsp] tells you that you can use one of those four letters as a command option -- i.e., a way of modifying the way the command works. In the "DESCRIPTION" section of the man page you will see a longer description of the command and an explanation of the options. Anything shown in the command synopsis which is contained within square brackets ([ ]) is optional. That's why it is ok to type "finger" with no options and no user. What about "user" -- what is that? To see what that means, quit out of the man page and type the following at the command prompt:

$ whoami

Let's say your username is osu0000. Then the result of the "whoami" command is osu0000. Now enter the following command (but replace osu0000 with your username):

$ finger osu0000

You should get information about yourself and no other users. You can also enter any of the usernames that are output when you enter the "finger" command by itself. The user names are in the leftmost column of output. Now try

 

$ finger -l osu0000

$ finger -lp osu0000

$ finger -s osu0000 osu0001

For the last command, use your username and the username of some other username that shows up in the output of the "finger" command with no arguments.

Note that a unix command consists of three parts:

  • command
  • option(s)
  • argument(s)

You don't necessarily have to enter an argument (as you saw with the "finger" command) but sometimes a command makes no sense without an argument so you must enter one -- you saw this with the "man" command. Try typing

$ man man

and looking briefly at the output. One thing to notice is the synopsis -- there are a lot of possible options for the "man" command, but the last thing shown in the command synopsis is "name ..." -- notice that "name" is not contained in square brackets. This is because it is not optional -- you must enter at least one name. What happens if you enter two names?

$ man man finger

The first thing that happens is you get the man page for the "man" command. What happens when you quit out of the man page? You should now get the man page for the "finger" command. If you quit out of this one you will be back at the shell prompt.

Combining Commands

You can "pipe" the output of one command to another. First, let's learn about the "more" command:

$ man more

Read the "DESCRIPTION" section -- it says that more is used to page through text that doesn't fit on one screen. It also recommends that the "less" command is more powerful. Ok, so let's learn about the "less" command:

$ man less

You see from the description that "less" also allows you to examine text one screenful at a time. Does this sound familiar? The "man" command actually uses the "less" command to display its output. But you can use the "less" command yourself. If you have a long text file named "foo.txt" you could type

$ less foo.txt

and you would be able to examine the contents of the file one screen at a time. But you can also use "less" to help you look at the output of a command that prints more than one screenful of output. Try this:

$ finger | less

That's "finger" followed by a space followed by the vertical bar (shifted backslash on most keyboards) followed by a space followed by "less" followed by <Enter>. You should now be looking at the output of the "finger" command in an interactive fashion, just as you were looking at man pages. Remember, to scroll use the arrow keys, the <Page Up> and <Page Down> keys, the <Enter> key or the space bar; and to quit, type "q".

Now try the following (but remember to replace "osu0000" with your actual username):

$ finger | grep osu0000

The "grep" command is Unix's command for searching. Here you are telling Unix to search the output of the "finger" command for the text "osu0000" (or whatever your username is.)

If you try to pipe the output of one command to a second command and the second is a command which works with no arguments, you won't get what you expect. Try

$ whoami | finger

You see that it does not give the same output as

$ finger osu0000

(assuming "whoami" returns osu0000.)

In this case what you can do is the following:

$ finger `whoami`

That's "finger" space backquote "whoami" backquote. The backquote key is to the left of the number 1 key on a standard keyboard.

apropos

Enter the following command:

$ man apropos

As you can see, the apropos searches descriptions of commands and finds commands whose descriptions match the keyword you entered as the argument. That means it outputs a list of commands that have something to do with the keyword you entered. Try this

$ apropos

Ok, you need to enter an argument for the "apropos" command.

So try

$ apropos calendar

Now you see that among the results are two commands -- "cal" and "difftime" that have something to do with the keyword "calendar."

Batch Tutorial

Description

This tutorial guides you through the process of creating and submitting a batch script on one of our compute clusters. This is a linux tutorial which uses batch scripting as an example, not a tutorial on writing batch scripts. The primary goal is not to teach you about batch scripting, but for you to become familiar with certain linux commands. There are other pages on the OSC web site that go into the details of submitting a job with a batch script.

Prerequisites

  • Familiarity with a text editor (emacs, nano, vim)
  • Basic understanding of the unix command line

Goals

  • Create subdirectories to organize information
  • Create a batch script with a text editor
  • Submit a job
  • Check on the progress of the job
  • Change the permissions of the output files
  • Get familiar with some common unix commands

Step 1 - Organize your directories

When you first log in to Glenn or Oakley, you are in your home directory. For the purposes of this illustration, we will pretend you are user osu0001 and your nfs file server number is 01, but when you try out commands you must use your own username and nfs file server number.

$ pwd
/nfs/01/osu0001
 
Note: you will see your user name and a different number after the /nfs.
 
It's a good idea to organize your work into separate directories. If you have used Windows or the Mac operating system, you may think of these as folders. Each folder may contain files and subfolders. The subfolders may contain other files and subfolders of their own. In linux we use the term "directory" instead of "folder." Use directories to organize your work.
 
Type the following four lines and take note of the output after each one:
 
$ touch foo1
$ touch foo2
$ ls
$ ls -l
$ ls -lt
$ ls -ltr
 
The "touch" command just creates an empty file with the name you give it.
You probably already know that the ls command shows the contents of the current working directory; that is, the directory you see when you type pwd. But what is the point of the "-l", "-lt" or "-ltr"? You noticed the difference in the output between just the "ls" command and the "ls -l" command.
Most unix commands have options you can specify that change the way the command works. The options can be specified by the "-" (minus sign) followed by a single letter. "ls -ltr" is actually specifying three options to the ls command.
l: I want to see the output in long format -- one file per line with some interesting information about each file
t: sort the display of files by when they were last modified, most-recently modified first
r: reverse the order of display (combined with -t this displays the most-recently modified file last -- it should be BatchTutorial in this case.)
 
I like using "ls -ltr" because I find it convenient to see the most recently modified file at the end of the list.
 
Now try this:
$ mkdir BatchTutorial
$ ls -ltr
 
The "mkdir" command makes a new directory with the name you give it. This is a subfolder of the current working directory. The current working directory is where your current focus is in the hierarchy of directories. The 'pwd' command shows you are in your home directory:
 
$ pwd
/nfs/01/osu0001
 
Now try this:
$ cd BatchTutorial
$ pwd
 
What is the output of 'pwd' now? "cd" is short for "change directory" -- think of it as moving you into a different place in the hierarchy of directories. Now do
$ cd ..
$ pwd
Where are you now?

Step 2 -- Get familiar with some more unix commands

Try the following:

$ echo where am I?
$ echo I am in `pwd`
$ echo my home directory is $HOME
$ echo HOME
$ echo this directory contains `ls -l`

These examples show what the echo command does and how to do some interesting things with it. The `pwd` means the result of issuing the command pwd. HOME is an example of an environment variable. These are strings that stand for other strings. HOME is defined when you log in to a unix system. $HOME means the string the variable HOME stands for. Notice that the result of "echo HOME" does not do the substitution. Also notice that the last example shows things don't always get formatted the way you would like.

Some more commands to try:

$ cal
$ cal > foo3
$ cat foo3
$ whoami
$ date

Using the ">" after a command puts the output of the command into a file with the name you specify. The "cat" command prints the contents of a file to the screen.

Two very important UNIX commands are the cp and mv commands. Assume you have a file called foo3 in your current directory created by the "cal > foo3" command. Suppose you want to make a copy of foo3 called foo4. You would do this with the following command:

$ cp foo3 foo4
$ ls -ltr

Now suppose you want to rename the file 'foo4' to 'foo5'. You do this with:

$ mv foo4 foo5
$ ls -ltr

'mv' is short for 'move' and it is used for renaming files. It can also be used to move a file to a different directory.

$ mkdir CalDir
$ mv foo5 CalDir
$ ls
$ ls CalDir

Notice that if you give a directory with the "ls" command is shows you what is in that directory rather than the current working directory.

Now try the following:

$ ls CalDir
$ cd CalDir
$ ls
$ cd ..
$ cp foo3 CalDir
$ ls CalDir

Notice that you can use the "cp" command to copy a file to a different directory -- the copy will have the same name as the original file. What if you forget to do the mkdir first?

$ cp foo3 FooDir

Now what happens when you do the following:

$ ls FooDir
$ cd FooDir
$ cat CalDir
$ cat FooDir
$ ls -ltr

CalDir is a directory, but FooDir is a regular file. You can tell this by the "d" that shows up in the string of letters when you do the "ls -ltr". That's what happens when you try to cp or mv a file to a directory that doesn't exist -- a file gets created with the target name. You can imagine a scenario in which you run a program and want to copy the resulting files to a directory called Output but you forget to create the directory first -- this is a fairly common mistake.

Step 3 -- Environment Variables

Before we move on to creating a batch script, you need to know more about environment variables. An environment variable is a word that stands for some other text. We have already seen an example of this with the variable HOME. Try this:

$ MY_ENV_VAR="something I would rather not type over and over"
$ echo MY_ENV_VAR
$ echo $MY_ENV_VAR
$ echo "MY_ENV_VAR stands for $MY_ENV_VAR"

You define an environment variable by assigning some text to it with the equals sign. That's what the first line above does. When you use '$' followed by the name of your environment variable in a command line, UNIX makes the substitution. If you forget the '$' the substitution will not be made.

There are some environment variables that come pre-defined when you log in to Glenn or Oakley. Try using 'echo' to see the values of the following variables: HOME, HOSTNAME, SHELL, TERM, PATH.

Now you are ready to use some of this unix knowledge to create and run a script.

Step 4 -- Create and run a script

Before we create a batch script and submit it to a compute node, we will do something a bit simpler. We will create a regular script file that will be run on the login node. A script is just a file that consists of unix commands that will run when you execute the script file. It is a way of gathering together a bunch of commands that you want to execute all at once. You can do some very powerful things with scripting to automate tasks that are tedious to do by hand, but we are just going to create a script that contains a few commands we could easily type in. This is to help you understand what is happening when you submit a batch script to run on a compute node.

Use a text editor to create a file named "tutorial.sh" which contains the following text (note that with emacs or nano you can use the mouse to select text and then paste it into the editor with the middle mouse button):

echo ----
echo Job started at `date`
echo ----
echo This job is working on node `hostname`

SH_WORKDIR=`pwd`
echo working directory is $SH_WORKDIR
echo ----
echo The contents of $SH_WORKDIR
ls -ltr
echo
echo ----
echo
echo creating a file in SH_WORKDIR
whoami > whoami-sh-workdir

SH_TMPDIR=${SH_WORKDIR}/sh-temp
mkdir $SH_TMPDIR
cd $SH_TMPDIR
echo ----
echo TMPDIR IS `pwd`
echo ----
echo wait for 12 seconds
sleep 12
echo ----
echo creating a file in SH_TMPDIR
whoami > whoami-sh-tmpdir

# copy the file back to the output subdirectory
cp ${SH_TMPDIR}/whoami-sh-tmpdir ${SH_WORKDIR}/output

cd $SH_WORKDIR

echo ----
echo Job ended at `date`

To run it:

$ chmod o+x tutorial.sh
$ ./tutorial.sh

Step 5 -- Create and run a batch job

Use your favorite text editor to create a file called tutorial.pbs in the BatchTutorial directory which has the following contents (remember, you can use the mouse to cut and paste text):

#PBS -l walltime=00:02:00
#PBS -l nodes=1:ppn=1
#PBS -N foobar
#PBS -j oe
#PBS -r n

echo ----
echo Job started at `date`
echo ----
echo This job is working on compute node `cat $PBS_NODEFILE`

cd $PBS_O_WORKDIR
echo show what PBS_O_WORKDIR is
echo PBS_O_WORKDIR IS `pwd`
echo ----
echo The contents of PBS_O_WORKDIR:
ls -ltr
echo
echo ----
echo
echo creating a file in PBS_O_WORKDIR
whoami > whoami-pbs-o-workdir

cd $TMPDIR
echo ----
echo TMPDIR IS `pwd`
echo ----
echo wait for 42 seconds
sleep 42
echo ----
echo creating a file in TMPDIR
whoami > whoami-tmpdir

# copy the file back to the output subdirectory
pbsdcp -g $TMPDIR/whoami-tmpdir $PBS_O_WORKDIR/output

echo ----
echo Job ended at `date`
 
To submit the batch script, type
$qsub tutorial.pbs
Use qstat -u [username] to check on the progress of your job. If you see something like this
$qstat -u osu0001

                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar              --      1      1    --  00:02 Q   --
 
this means the job is in the queue -- it hasn't started yet. That is what the "Q" under the S column means.
 
If you see something like this:
                                                                             Req'd  Req'd   Elap
Job ID             Username    Queue    Jobname          SessID NDS   TSK    Memory Time  S Time
------------------ ----------- -------- ---------------- ------ ----- ------ ------ ----- - -----
458842.oak-batch   osu0001     serial   foobar            26276     1      1    --  00:02 R   --
this means the job is running and has job id 458842.
 
When the output of the qstat command is empty, the job is done.
 
After it is done, there should be a file called "foobar.o458842" in the directory.
Note that your file will end with a different number -- namely the job id number assigned to your job.
Check this with
$ ls -ltr
$ cat foobar.oNNNNNN

Where (NNNNNN is your job id).

The name of this file is determined by two things:
  1. The name you give the job in the script file with the header line #PBS -N foobar
  2. The job id number assigned to the job.

The name of the script file (tutorial.pbs) has nothing to do with the name of the output file.

Examine the contents of the output file foobar.oNNNNNN carefully. You should be able to see the results of some of the commands you put in tutorial.pbs. It also shows you the values of the variables PBS_NODEFILE, PBS_O_WORKDIR and TMPDIR. These variables exist only while your job is running. Try

$ echo $PBS_O_WORKDIR

and you will see it is no longer defined. $PBS_NODEFILE is a file which contains a list of all the nodes your job is running on. Because this script has the line

#PBS -l nodes=1:ppn=1

the contents of $PBS_NODEFILE is the name of a single compute node.

Notice that $TMPDIR is /tmp/pbstmp.NNNNNN (again, NNNNNN is the id number for this job.) Try

$ ls /tmp/pbstmp.NNNNNN

Why doesn't this directory exist? Because it is a directory on the compute node, not on the login node. Each machine in the cluster has its own /tmp directory and they do not contain the same files and subdirectories. All machines see the same /nfs/18/jeisenl but not the same /tmp. This goes for all the login and compute nodes on both Glenn and Oakley. Repeat: the /nfs directories are shared by all the nodes (login or compute) but each node has its own /tmp directory (as well as other unshared directories.)

Tar Tutorial

Prerequisites

Step 1 -- Create a directory to work with and download a "tarball"

Start off with the following:

$ mkdir TarTutorial
$ cd TarTutorial
$ wget http://www.mmm.ucar.edu/wrf/src/WRFDAV3.1.tar.gz
$ ls -ltr

The third command will take a while because it is downloading a file from the internet. The file is call a "tarball" or a "gzipped tarball". TAR is an old unix short name for "tape archive" but a tar file is a file that contains a bunch of other files. If you have to move a bunch of files from one place to another, a good way to do it is to pack them into a tar file, move the tar file where you want it then unpack the files at the destination. A tar file usually has the extension ".tar". What about the ".gz"? This means the tar file has been further compressed with the program gzip -- this makes it a lot smaller.

Step 2 -- Unpack the "tarball" and check out the contents

After step 1 your working directory should be ~/TarTutorial and there should be a file called WRFDAV3.1.tar.gz in it.

Now do this:

$ gunzip WRFDAV3.1.tar.gz
$ ls -ltr

You should now have a file called WRFDAV3.1.tar which should be quite a bit larger in size than WRFDAV3.1.tar.gz -- this is because it has been uncompressed by the "gunzip" command which is the opposite of the "gzip" command.

Now do this:

$ tar -xvf WRFDAV3.1.tar
$ ls -ltr

You should see a lot of filenames go by on the screen and when the first command is done and you issue the ls command you should see two things -- WRFDAV3.1.tar is still there but there is also a directory called WRFDA. You can look at the contents of this directory and navigate around in the directory tree to see what is in there. The options on the "tar" command have the following meanings (you can do a "man tar" to get all the options):

x: extract the contents of the tar file

v: be verbose, i.e. show what is happening on the screen

f: the name of the file which follows the "f" option is the tar file to expand.

Another thing you can do is see how much space is being taken up by the files. Make sure TarTutorial is your working directory then issue the following command:

$ du .

Remember that "." (dot) means the current working directory. The "du" command means "disk usage" -- it shows you how much space is being used by every file and directory in the directory tree. It ends up with the highest level files and directories. You might prefer to do

$ du -h .
$ ls -ltrh

Adding the "-h" option to these commands puts the file sizes in human-readable format -- you should get a size of 66M for the tar file -- that's 66 megabytes -- and "du" should print a size of 77M next to ./WRFDA.

Step 3 -- create your own "tarball"

Now, make your own tar file from the WRFDA directory tree:

$ tar -cf mywrf.tar WRFDA
$ ls -ltrh

You have created a tar from all the files in the WRFDA directory. The options given to the "tar" command have the following meanings:

c: create a tar file

f: give it the name which follows the "f" option

The files WRFDAV3.1.tar and mywrf.tar are identical. Now compress the tar file you made:

$ gzip mywrf.tar
$ ls -ltrh

You should see a file called mywrf.tar.gz which is smaller than WRFDAV3.1.tar.

Step 4 -- Clean up!

You don't want to leave all these files lying around. So delete them

$ rm WRFDAV3.1.tar
$ rm mywrf.tar
$ rm WRFDA

Oops! You can't remove the directory. You need to use the "rmdir" command:

$ rmdir WRFDA

Oh no! That doesn't work on a directory that's not empty. So are you stuck with all those files? Maybe you can do this:

$ cd WRFDA
$ rm *
$ cd ..
$ rmdir WRFDA

That won't work either because there are some subdirectories in WRFDA and "rm *" won't remove them. Do you have to work your way to the all the leaves at the bottom of the directory tree and remove files then come back up and remove directories? No, there is a simpler way:

$ rm -Rf WRFDA

This will get rid of the entire directory tree. The options have the following meanings:

R: recursively remove all files and directories

f: force; i.e., just remove everything without asking for confirmation

I encourage you to do

$ man rm

and check out all the options. Or some of them -- there are quite a few.

 

Unix Shortcuts

Description

This tutorial shows you some handy time-saving shortcuts in linux. Once you have a good understanding of how the command line works, you will want to learn how to work more efficiently.

Prerequisites

Linux command line fundamentals.

Goals

  • Save you time when working on a linux system
  • Increase your appreciation of the power of linux

Step 1 -- The Arrow Keys

Note: even if you know how to use the up arrow in linux, you need to enter the commands in this section because they are used in the following sections. So to begin this tutorial, go to your home directory and create a new directory called ShortCuts:

$ cd
$ mkdir Shortcuts
$ cd Shortcuts

(If a directory or file named "Shortcuts" already exists, name it something else.)

Imagine typing in a long linux command and making a typo. This is one of the frustrating things about a command line interface -- you have to retype the command, correcting the typo this time. Or what if you have to type several similar commands -- wouldn't it be nice to have a way to recall a previous command, make a few changes, and enter the new command? This is what the up arrow is for.

Try the following:

$ cd ..
$ cd ShortCuts (type a capital C)

Linux should tell you there is no directory with that name.

Now type the up arrow key -- the previous command you entered shows up on the command line, and you can use the left arrow to move the cursor just after the capital C, hit Backspace, and type a lower case c. Note you can also position the cursor before the capital C and hit Delete to get rid of it.

Once you have changed the capital C to a lower case c you can hit Return to enter the command -- you do not have to move the cursor to the end of the line.

Now hit the up arrow key a few times, then hit the down arrow key and notice what happens. Play around with this until you get a good feel for what is happening.

Linux maintains a history of commands you have entered. Using the up and down arrow keys, you can recall previously-entered commands to the command line, edit them and re-issue them.

Note that in addition to the left and right arrow keys you can use the Home and End keys to move to the beginning or end of the command line. Also, if you hold down the Ctrl key when you type an arrow key, the cursor will move by an entire word instead of a single character -- this is useful is many situations and works in many editors.

Let's use this to create a directory hierarchy and a few files. Start in the Shortcuts directory and enter the following commands, using the arrow keys to simplify your job:

$ mkdir directory1
$ mkdir directory1/directory2
$ mkdir directory1/directory2/directory3
$ cd directory1/directory2/diectoryr3  (remember the Home key and the Ctrl key with left and right arrows)
$ hostname > file1
$ whoami > file2
$ mkdir directory4
$ cal > directory4/file3

Step 2 -- Using the TAB key

Linux has short, cryptic command names to save you typing -- but it is still a command line interface, and that means you interact with the operating system by typing in commands. File names can be long, directory hierarchies can be deep, and this can mean you have to type a lot to specify the file you want or change to current working directory. Not only that, but you have to remember the names of files and directories you type in. The TAB key gives you a way to enter with commands with less typing and less memorization.

Go back to the Shortcuts directory:

$ cd
$ cd Shortcuts

Now enter the following:

$ hostname > file1
$ cal > file2
$ whoami > different-file
$ date > other-file
$ cal > folio5

Now type the following, without hitting the Return key:

$ cat oth <Tab>

What happened? Linux completed the name "other-file" for you! The Tab key is your way of telling Linux to finish the current word you are typing, if possible. Because there is only one file in the directory whose name begins with "oth", when you hit the Tab key Linux is able to complete the name.

Hit Return (if you haven't already) to enter the cat command. Now try

$ cat d <Tab>

As you would expect, Linux completes the name "different-file"

What if you enter

$ cat fi <Tab>

Notice Linux completes as much of the name as possible. You can now enter a "1" or a "2" to finish it off.

But what if you forget what the options are? What if you can't remember if you created "file1" and "file2" or if you created "fileA" and fileB"?

With the comman line showing this:

$ cat file

hit the Tab key twice. Aha! Linux shows you the possible choices for completing the word.

Try

$ cat f <Tab>

The Tab will not add anything -- the command line will still read

$ cat f

Now type the letter o followed by a Tab -- once you add the o there is only one possible completion -- "folio".

Now enter the following:

$ cat directory1/directory2/directory3/directory4/file3

That's kind of a painful to type.

Now type the following without entering Return:

$ ls dir <Tab>

Nice! As you would expect, Linux completes the name of the directory for you. This is because there is only one file in the Shortcuts directory whose name begins with "dir"

Hit Return and Linux will tell you that directory1 contains directory2.

Now type this:

$ ls dir <Tab>

and before you hit return type another d followed by another Tab. Your command line should now look like this:

$ ls directory1/directory2/

If you hit Return, Linux will tell you that directory2 contains directory3.

Now try this:

$ ls dir <Tab>

then type another d followed by <Tab> then another d followed by tab. Don't hit Return yet. Your command line should look like this:

$ ls directory1/directory2/directory3/

Don't hit Return yet. Now type the letter f followed by a Tab. What do you think should happen?

Step 3 -- The Exclamation Point

Hitting the up arrow key is a nice way to recall previously-used commands, but it can get tedious if you are trying to recall a command you entered a while ago -- hitting the same key 30 times is a good way to make yourself feel like an automaton. Fortunately, linux offers a couple of other ways to recall previous commands that can be useful.

Go back to the Shortcuts directory

$ cd ~/Shortcuts

and enter the following:

$ hostname
$ cal
$ date
$ whoami

Now enter this:

$ !c

and hit return.

What happened? Now try

$ !h

and hit return.

The exclamation point ("bang" to Americans, "shriek" to some Englishmen I've worked with) is a way of telling linux you want to recall the last command which matches the text you type after it. So "!c" means recall the last command that starts with the letter c, the "cal" command in this case. You can enter more than one character after the exclamation point in order to distinguish between commands. For example if you enter

$ cd ~/Shortcuts
$ cat file1
$ cal
$ !c

the last command will redo the "cal" command. But if you enter

$ cat file1
$ cal
$ !cat

the last command re-executes the "cat" command.

Step 4 -- Ctrl-r

One problem with using the exclamation point to recall a previous command is that you can feel blind -- you don't get any confirmation about exactly which command you are recalling until it has executed. Sometimes you just aren't sure what you need to type after the exclamation point to get the command you want.

Typing Ctrl-r (that's holding down the Ctrl key and typing a lower case r) is another way to repeat previous commands without having to type the whole command, and it's much more flexible than the bang. The "r" is for "reverse search" and what happens is this. After you type Ctrl-r, start typing the beginning of a previously entered command -- linux will search, in reverse order, for commands that match what you type. To see it in action, type in the following commands (but don't hit <Enter> after the last one):

$ cd ~/Shortcuts
$ cat file1
$ cat folio5
$ cal
$ Ctrl-r cat

You should see the following on your command line:

(reverse-i-search)`cat': cat folio5

Try playing with this now. Type in " fi" (that's a space, an "f" and an "i") -- did the command shown at the prompt change? Now hit backspace four times.

Now enter a right or left arrow key and you will find yourself editing the matching command. This is one you have to play around with a bit before you understand exactly what it is doing. So go ahead and play with it.

Step 5 -- history

Now type

$ history

and hit return.

Cool, huh? You get to see all the commands you have entered (probably a maximum of 1000.) You can also do something like

$ history | grep cal

to get all the commands with the word "cal" in them. You can use the mouse to cut and paste a previous command, or you can recall it by number with the exclamation point:

$ !874

re-executes the command number 874 in your history.

For more information about what you can do to recall previous commands, check out http://www.thegeekstuff.com/2011/08/bash-history-expansion/

Step 6 -- Ctrl-t

I am just including this because to me it is a fun piece of linux trivia. I don't find it particularly useful. Type

$ cat file1

and hit <Return>. Now hit the up arrow key to recall this command and hist the left arrow key twice so the cursor is on the "e" of "file1". Now hit Ctrl-t (again, hold down the control key and type a lower case t.) What just happened? Try hitting Ctrl-t a couple more times. That's right -- it transposes two characters in the command line -- the one the cursor is on and the one to its left. Also, it moves the cursor to the right. Frankly, it takes me more time to think about what is going to happen if I type Ctrl-t than it takes me to delete some characters and retype them in the correct order. But somewhere out there is a linux black belt who gets extra productivity out of this shortcut.

Step 7 -- The alias command

Another nice feature of linux is the alias command. If there is a command you enter a lot you can define a short name for it. For example, we have been typing "cat folio5" a lot in this tutorial. You must be getting sick of typing "cat folio5". So enter the following:

$ alias cf5='cat folio5'

Now type

$ cf5

and hit return. Nice -- you now have a personal shortcut for "cat folio5". I use this for the ssh commands:

$ alias gogl='ssh -Y jeisenl@glenn.osc.edu'

I put this in the .bash_aliases file on my laptop so that it is always available to me.