Astronomy 480 66 Linux Tutorial II
A brief review
Changing directories using command lines in a terminal
You can tell where you are in the directory structure by typing pwd
Here is part of what I have in my directory
/astro/users/larson/ [directories are shown in bold]
Figure 1
7larsonBastrolab18 ~!" pwd
/users/larson
7larsonBastrolab18 ~!" ls
1979PASP...91..589B.pdf.gz
PG1528+062.ps
login.cl.OLD
30536-25.JPG
celestial2mechanics
m13CMD.ps
5085.pdf
celm13.pdf
m57c001.FIT
Astro480
clusters_dao_stromgren.sxc
mail
BV.ps
daophot2.ps
manuals
The cd command moves you around in the directory structure, and takes an argument that is the desired destination
directory. The argument can be either a relative or an absolute pathname. If I were already in the "larson" directory
shown in Fig. 1 above, and I wanted to move into the directory called "
Astro480" I would simply type:
cd Astro480
and the system would move my current working directory to
/users/larson/Astro480/. If I wanted to move to this
directory from somewhere other than the directory right above it (also called the parent directory) I could use an
absolute pathname by typing:
cd /users/larson/Astro480
Linux provides some useful shortcuts for navigating directories. A single dot, ".", always refers to the current directory.
Double dots, ".." refer to the parent directory. To move up two levels in the directory structure, you would type:
cd ../../
The tilde symbol, "~", is a shorthand for home directories. If you wanted to move to my home directory, from anywhere
in the directory structure, you would type:
cd ~larson
You can always get back to your home directory by typing cd with no arguments.
Listing the contents of a directory using command lines
The command ls is used to list the contents of a directory. Under Linux, files, directories and even devices (such as the
CD drive) are treated as philosophically equal, so a directory could contain any one of these types of items. The ls
command can be invoked with a variety of options, which modify its action. Under Linux, command options are
preceded by a hyphen. A few of the more useful forms of ls include:
ls –l generates a full listing, including dates, sizes, etc.
ls –p distinguishes between directories and regular files
ls –a lists all files, including those that begin with a ".", which are otherwise hidden files.
ls –t lists contents by date of their creation, latest first.
You can combine them, so for example
ls –apt
is perfectly valid.
Filenames and Wildcards
Files in the current working directory can be referred to simply by their filename. In general,
however, the name of a file includes its full pathname, such as
/users/larson/foo.txt
where the last element, foo.txt, is the file name.
Linux allows you to select a subset of the objects of interest, using wildcards and range restrictions.
For example, to obtain a listing of all files that end in ".doc", you would type:
ls *.doc
Similarly, the character "?" in a filename allows for any
single character to occupy that position in
the file name. If I had a list of successive astronomical images called
obj.001.fits through
obj.120.fits and I wanted only those in the range 120-129, I could use:
ls obj.12?.fits
You can also specify a range of characters and numbers, by enclosing the range in square brackets.
To get a list of all images with numbers between 111 and 119 I could use:
ls obj.1[11-19].fits
Copying Files: cp
To copy a file, use the cp command. The cp has the following syntax:
cp [options] source destination
source is the name of the file you want to copy, and destination is the name of the copy you
create.
If destination is a directory (the path didn't specify a filename), the file is copied with its original name into the
specified directory.
The options argument is shown between brackets to say that options are optional. We'll use an option on the cp
command in the next section.
Here's an example:
[alberto@digital alberto]$ ls -F
Xrootenv.0 afile
anotherlink helloworld*
adir/
alink@ hello
[alberto@digital alberto]$ cp helloworld /tmp
[alberto@digital alberto]$ ls -F /tmp
fvwmrca00455 helloworld* install.log screens/
You can copy multiple files to a single directory in a single command by listing several source files separated by
spaces. The only requirement is that the last argument (destination) be a directory.
Copying Directories
You copy directories in much the same way you copy files. When copying directories you need to tell cp that you want
to copy recursively all the files and directories
contained by the source directory. This is easily done with the -R option. The syntax looks like this:
[alberto@digital alberto]$ ls
Xrootenv.0 adir/
afile
alink@ anotherlink
helloworld*
[alberto@digital alberto]$ cp -R adir /tmp
[alberto@digital alberto]$ ls /tmp
adir/
install.log
Moving Files and Directories: m
To move a file or directory, you use the mv command. Moving files is similar to copying files. The big difference is
that the original file is removed after the new copy is created. The mv command follows this syntax:
mv [options] source destination
[alberto@digital alberto]$ ls
Xrootenv.0 adir/
afile
alink@ anotherlink
helloworld*
[alberto@digital alberto]$ mv afile file2
[alberto@digital alberto]$ ls
Xrootenv.0 adir/
alink@ anotherlink file2
helloworld*
The mv command can also be used to move an entire directory tree.
The mv command provides several options. For more information, refer to its manual page.
Copying Files
The command cp is used to copy files. The syntax of this command conforms to the (almost)
general UNIX standard of:
omman source destination
so for example I could make a backup copy of the file foo.txt by typing
cp foo.txt foo.bak
Creating Directories
You can create a new directory just below the current working directory by using the command
mkdir
name, where
name is the name of the directory you want to create. Avoid spaces in
directory names, Linux hates spaces in directory and file names and lets you know it!
Directories are deleted with the rmdir command. The directories will need to be empty before
they can be removed. Feeling vicious? Try this on a directory where you do not want what’s in it:
\rm –R
directoryname/*
rmdir
directoryname
The backslash in \rm tells Linux you don’t want confirmation before removing files, and, in this
case, subdirectories and everything in them. Once gone, files and directories cannot be retrieved
unless they were backed-up. There’s no menu that you can go to that says “undelete.” Trust me, I
know.
iewing the Contents of a File
The commands cat
file and more
file print the contents of a simple text file to the screen. The cat
command scrolls the entire thing past with no pauses. The command more allows you to page
through the file, using the spacebar to move one screenful and the Enter key to move down one line
at a time. Less is even more flexible as you can search that file and move up and down, mark your
place, plus more. You should type the following:
man less
and read what it says. By the way, if you need help on some topic and do not know the exact
command name, or command that involves what you want to do, use:
man –k
whatIwanttoknowabout
Try:
man image
and then:
man –k image
and see what we mean.
Here are a couple more handy commands (see
man pages for available flags):
♦
ea-Peek at the first few lines in a file.
♦
2ail-Peek at the last few lines in a file.
Redirection & Saving our Output
One of the most useful aspects of Linux is the ability to redirect streams of information, input and
output to and from files and processes. The symbols , and are used to accomplish this. For
example, to send the listing of all the files in the current directory into a file called foo, one would
type:
ls –a > foo
This has the feature that if a file called foo existed already,
it would be overwritten with the new
information. You could instead append the directory listing to a pre-existing file called foo by using
ls –a >> foo
File Ownership and Permissions
Let’s return for a moment to this idea of owning a directory or a file and being able to set
permissions for others.
- rwx rwx rwx 1 larson astro-480 1327 Mar 28 2005 pegasus.txt
What if you wanted others to be able to read your files but not be able to write, change, or execute
any of them? Take a look at this listing from
/net/projects/Astro2480/spring-06/larson/exercise1
- rw- r-- r-- 1 larson astro-480 1546126 Feb 27 18:42 flat.0001.fits.g
It is a file, the owner can read and write but not execute (but it’s not executable anyway), the group
can only read the file (or copy it to their directory, but not move nor delete), the world can only read
the file. There may be cases where you cannot get a file I have requested you get from one of my
directories. I can fix that in a jiffy with the command
chmod. Do the following in your directory:
[larson¿astrolab18 test]$ touch trialfile
¿create an empty file by ‘touch’
[larson¿astrolab18 test]$ ls -l
-rwxrwxrwx 1 larson astro-480 73 Apr 4 2005 bill
-rw-rw-rw- 1 larson astro-480 954164 Apr 4 2005 out.txt
-rw-rw-r-- 1 larson astro-480 0 Mar 28 18:16 trialfile
¿default permissions
[larson¿astrolab18 test]$ chmod ug-w trialfile
¿prevent writes by everyone, even you
[larson¿astrolab18 test]$ ls -l
-rwxrwxrwx 1 larson astro-480 73 Apr 4 2005 bill
-rw-rw-rw- 1 larson astro-480 954164 Apr 4 2005 out.txt
-r--r--r-- 1 larson astro-480 0 Mar 28 18:16 trialfile
[larson¿astrolab18 test]$ chmod ug+x trialfile
¿make it executable
[larson¿astrolab18 test]$ ls -l
-rwxrwxrwx 1 larson astro-480 73 Apr 4 2005 bill
-rw-rw-rw- 1 larson astro-480 954164 Apr 4 2005 out.txt
-r-xr-xr-- 1 larson astro-480 0 Mar 28 18:16 trialfile
[larson¿astrolab18 test]$ chmod ug+w trialfile
¿add write back in
[larson¿astrolab18 test]$ ls -l
-rwxrwxrwx 1 larson astro-480 73 Apr 4 2005 bill
-rw-rw-rw- 1 larson astro-480 954164 Apr 4 2005 out.txt
-rwxrwxr-- 1 larson astro-480 0 Mar 28 18:16 trialfile
owner can rwx
plain file
group can rwx
others (world) can rwx
owner
group
Troubleshooting
If you find that the cursor has gone away, with no indication of ever returning, try the old standby
CTRL-c. This means hold down the Ctrl key and hit "c". This ought to kill the hung process. If this
fails, try CTRL-z, where you hit "z" instead of "c". This suspends, rather than kills, the hung
process but still might let you recover. Then, you have to get rid of the hung process, but we’ll
figure that out later.
Remember, never just turn a Linux machine off with the on-off button, or you truly will be an idiot.
Filename Expansion: Tab
As I said earlier, shells are not very ergonomic, and most people don't like to type commands or long
pathnames very often. Depending on the shell of you use, you might have the ability to have the shell
complete filenames and command names for you. The shell will do this whenever the portions of the
path you specified cannot be confused for something else.
To activate completion on bash, all you need to do is press
Tab after you've typed enough
characters. If you wanted a listing of the /usr/local/bin directory, you could type
ls
/uΠab /loΠab /bΠab, and the shell will expand each of the paths for you, saving you some keystrokes.
If the shell cannot complete the expansion because multiple completions are possible, hitting
Tab again will list
everything that could be a match. This is very useful if you have forgotten the name of a command. For example if you
type
lΠab Πab, the shell will respond with a list of all the programs that begin with an l.
More Wor ing with Files and Folders
Creating some necessary directories
You will now need to go to your course directory and use the mkdir command to set up a sub-
directory for your first exercise in IRAF: exercise1
That will be enough to get us started. Although we will not be starting our IRAF work just yet, we
can set up the directory for the first exercise. Change directories so that you are in your ‘exercise1’
directory. Copy the necessary files from
/net/projects/Astro2480/spring-06/larson/exercise1
by using a relative path:
cp ../larson/exercise1/*.gz .
¿there is a space after gz
[If this path doesn’t work, figure out why not!] How many parts of the command do you recognize?
What you have told the computer is to “
go up one directory, over to larson, down to exercise1, grab
everything that ends in .gz and copy it to the directory am currently in exactly as everything was
where it is being copied from (that’s what the period at the end does).” Whew.
See what is now in your directory. These files are compressed, or ‘zipped’ (gzipped to be precise).
We will leave them in that state for now.
Reading files
You’ve already been introduced to a bit of this. Copy the following file into a directory (preferably
not the ‘exercise1’ one you just created): /users/larson/pegasus.txt
Do the following things to that file:
cat pegasus.txt
less pegasus.txt
head pegasus.txt
head -10 pegasus.txt
tail pegasus.txt
tail -5 pegasus.txt
cat pegasus.txt > temp
cat pegasus.txt >> temp
cat -n pegasus.txt
[OK, are you using the tab key to shorten the number of strokes you use? Are you using the up-
arrow key when you repeat all or part of a command?]
Text diting Under a Shell
Vi (now known as
vim) will be popping up unexpectedly for us in IRAF. You need to be able to
recognize that that is what is happening and know how to edit a file within vi. Some may think that
“vi” stands for very idiotic, but it has its time and place as an editor. It is fast, no new windows pop
open, and only a few keystrokes get the job done. But, it is definitely not very sophisticated. We
will work through a short tutorial here first. Then, we will move onto a more powerful editor called
Emacs.
im Basics
Vim is a modal editor. All this means is that when you are using vim, the program behaves differently depending on
whether you are in command mode or editing mode.
Let's go. Edit the Pegasus.txt file with vim. On your command line, issue the following:
vim Pegasus.txt
~
~
~
~
"pegasus.txt" 21L, 1327C
On issuing the command, the editor takes over your terminal. Empty lines are marked by a tilde character. [The tildes
are the most obvious evidence that you are in vi¿ the other is that you won’t be able to change anything until you get
into the edit mode.] Vim is currently in its command mode. It is waiting for you to tell it what to do.
When in command mode, you can move around the document (assuming there's some text to navigate, which won't be
the case in a new document) and issue commands. Table 13.1 lists all the cursor moving commands. (As you can see,
some are mapped to special keys on your keyboard.)
Table 13.1 Moving Around the Document
Key
Function
l or Right Arrow
Move forward to the next character
h or Left Arrow
Move back one character
j or Down Arrow
Move down one line
k or Up Arrow
Move up one line
w
Move one word forward
b
Move one word backward
In general, you move your cursor by using the arrow keys (or their
—l counter-parts).
[You can move quickly around the document by using [ ir or ] or A. You can search for a string by using /
searchstring
to search down or ?
searchstring to search up.]
The cursor will not wrap or move beyond the beginning or end of a line. When you reach the end, the computer beeps.
To go to the next or previous line, use the down-or up-arrow keys, respectively.
When you begin a new, blank document, you don't have much to do¿ there's no text to edit or navigate. To add text, you
need to get into the insert mode. This mode allows you to enter text as you normally do in other programs¿ you are still
able to use the arrow keys to move around. (The
—l keys type a letter when you are in insert mode.) Type
i to get
into the insert mode. Table 14.2 lists a number of editing commands that you can use while in command mode.
Table 14.2 i ( im) diting Commands
Command
Description
i
Insert text (begin editing)
x
Delete the character under the cursor (command mode)
dw
Delete characters until the end of the word
d$
Delete text until the end of the line
dd
Delete the current line
u
Undo the last command
U
Undo any changes to the line
Ctrl+R
Redo any undos
Esc
Return to command mode, cancel current action-repeat until vim beeps
To return to the command mode, hold down the
sc key until vim beeps at you. Then you can type a :+command.
Commands are issued by pressing the colon followed by the name of the command. Table 14.3 lists the basic ones to get
you out of vim.
Table 14.3 i ( im) xiting Commands
Command
Description
:q!
uit without saving
:wq
Save the file and quit
:w
filename
Save the buffer to
filename
Vim has some editing commands, and the all-important undo. These editing commands work while vim is in command
mode.
diting with macs
From the Idiot’s Guide: “Many hardcore UNIX people use only one program: Emacs. They start it
when they start their work session, and they close it when they exit their system. All their work,
with rare exceptions, is handled through Emacs, including access to the shell.” This is very true for
a great number of astronomers. Emacs is much more powerful than vi, especially if you are a
programmer. I recommend you take the time to work through the on-line tutorial when you have
the chance. We won’t take any class time on it. Here’s a quick summary:
XEmacs is the variant of Emacs, the GNU super editor, included with Caldera OpenLinux. XEmacs
provides additional enhancements when used under a graphical environment, such as X (KDE),
hence its "X" denomination. Under a terminal, it is almost exactly the same as regular Emacs. Any reference to Emacs
applies in terms of usage to XEmacs.
Emacs is the most powerful of editors. It is available for UNIX, Windows, and a slew of other operating systems. It
provides features too numerous to cover in 500 pages just dedicated to Emacs alone!
Emacs is an extensible editor. Using a programming language called Lisp, Emacs can be easily extended to do just
about anything thinkable.
Many hardcore UNIX people use only one program: Emacs. They start it when they start their work session, and they
close it when they exit their system. All their work, with rare exceptions, is handled through Emacs, including access to
the shell.
From Emacs you can read, write, and organize your email and calendar, manipulate and organize your files, browse the
Web, read news, develop software, transfer FTP files across the network, and much more. No matter what you do under
UNIX, it is likely that you can do it through Emacs. Of course, Emacs also edits files. If you get the sense that Emacs is
really an environment, you are correct. That is what separates Emacs from other editors.
Emacs does everything through modes. A
mode is just a specialized interface for interacting with a specific program or
for working with a specific file format such as text or programming source code. Modes are tailored to the needs of a
particular task. It may sound complicated, but it really isn't. The modes are automatically handled by Emacs depending
on what you are doing and the file you are editing.
Starting Emacs and the Emacs Tutorial
To enter Emacs (XEmacs), just type
Œema s at the command prompt. Emacs greets you with a welcome message and
a list of options. Most keystrokes under Emacs work as follows:
Ctrl+letter letter
When you see a command listed as
Œ2 , it means that first you must press
Ctrl¢t and then
h by itself. Yes, Emacs
has a lot of command keys, and it requires a little time to get used to it¿ however, that is time well spent.
To exit Emacs, press
Ctrl¢c Ctrl¢xA this returns you to your shell. Teaching Emacs is beyond the scope of this book,
but suffice it to say that it is worth exploring if you are going to do a lot of text editing.
One impressive feature of Emacs is that you can edit files through FTP as if they were local on your disk. For users
working on Web-related services, this feature rocks. If your files can be reached through FTP, they can be edited and
manipulated just as if they were local files. However, that is an advanced topic for another book.
If you are a programmer, Emacs does source formatting on-the-fly, so your source code is always formatted in a way
that you can read. When reading other people's code, the ability to reformat the code in a way readable to you is
invaluable. Emacs also provides an IDE (Integrated Development Environment): You can build your program and
debug it right from Emacs.
Emacs also has an online tutorial. To access the tutorial, start Emacs, and in the
welcome window type
Π2 (press
Ctrl¢h, and then press
t).
During riday≥s long class period, we will be working with more complicated features of inux
(after a bit of review) and getting our directories and control files set up for running R . ¨e will
also be working on your first assignment that will be turned in and graded that will test your
proficiency with some of the fundamentals of inux.
