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Working with Files

All information on Athena is stored in files that are organized into directories. A file is simply a bunch of data associated with a name (the filename). Most of the things you do on Athena affect files or their contents. Papers, programs, and mail messages are all stored in files. If you are going to use the Athena system to do any substantial work, you are going to create and manipulate files.

Directories (often called "folders" on other operating systems) provide a means of organizing files into meaningful groups. When you log in, you are placed in your home directory, which contains all your files. A few directories inside your home directory have already been created for you:

  • Public - files placed in this directory will be readable by anyone (not just at MIT, but anyone on the Internet)
  • Private - files placed in this directory are guaranteed (unless you change the permissions) to be unreadable by anyone except you
  • www - a location to create your personal website.
  • OldFiles - actually, this isn't a directory at all, but a backup copy of your account from the previous night. For more information, see: Q: What is the OldFiles directory?.

Mastering the basics of the operating system means learning how to create and manipulate files (and knowing how to get out of anything you may get into). This section explains how to manipulate files. A later section, Working with Directories explains how to maneuver around directories.

File Names

Directory and filenames can be up to 256 characters in length. You can use any character on the keyboard in a filename except a slash (/), but it is best to stick to a-z, A-Z, 0-9, the period or "dot" (.), and the underscore (_). If you use any other characters, you may be setting yourself up for serious trouble. Case matters in filenames: "myfile" is a different file from "Myfile".

File Naming Conventions

Filenames often have extensions. For example, in a file named foo.txt, the ".txt" is the extension. Files have extensions for two reasons:

  • An extension tells people something about a file.
  • Some programs require that the files they deal with have a certain extension; programming language compilers, for instance, require that language source files have proper extensions; .c for C, and so forth.

Some file names start with a . (dot), e.g., .cshrc or .startup.X. The only significance to this is that these files do not normally show up when you ask for a list of your files. Background, utility, and "start up" files, among others, are typically named this way, so you do not usually have to see them in file listings.

Wildcards: * and ?

The system provides a mechanism called wildcard characters which lets you refer to more than one file at once.

  • is one of the two most commonly used wildcard characters. It matches all files except those whose names begin with . (a period), or any number of characters within a filename. For example, *.f means "all filenames with a .f extension"; h.f and verylongfilename.f would both match. a* means "all filenames that begin with a"; a and anotherfilename.c would both match.

The other is ?, which matches single characters. ?.f means "all one-character filenames with a .f extension"; a.f would match, but ab.f would not.

Testing Wildcards with echo

One way to test out a file/directory list before you use it in an actual command is to use the echo command to find out what the system thinks you mean by a particular specification:

joeuser@athena:~$ echo specification

The echo command simply types out its arguments. When it is run, all wildcards are expanded into full filenames if any matching files exist. The actual files themselves are not touched.

For instance, suppose these were the contents of a directory:

joeuser@athena:~$ ls

If you wanted to remove the old version of the temps file (temps.old) using an abbreviated form, you could first test your file specification using the echo command:

joeuser@athena:~$ echo *old

Here you would find that your directory specification did not match what you intended. You could try again with a more precise specification:

joeuser@athena:~$ echo *.old

Now that you have confirmed that the specification refers to the files you want, you can use that specification in the actual command (such as delete) that you intended to use with confidence that the files referred to are the appropriate ones!

Creating and Displaying Files with the cat Command

The cat (for "concatenate") command displays the contents of a file (or any number of files) on the screen. Its command format is:

cat filename

For example, you can read the "welcome" file in your account (if you haven't already deleted it) with the following command:

joeuser@athena:~$ cat ~/welcome

The contents of the file are shown on the screen. If the file is very long, its contents will scroll past you faster than you can read them. You can type Ctrl-s to stop the screen from scrolling, and Ctrl-q to resume scrolling. To cancel a cat command and stop its output, type Ctrl-c.

If you don't specify a file, the cat command will wait for input from the keyboard. Using the concepts of I/O Redirection discussed earlier, this can be used as a quick way to create a small file. With this method, you just type the contents of the file at the keyboard. You can fix typing mistakes in the current line by deleting them; you can erase the current line by typing Ctrl-u, but you cannot change previous lines. When you are done, you finish the last line with a Return and then type Ctrl-d (it is displayed as ^D). For example:

joeuser@athena:~$ cat > shopping-list
Diet Coke
Hot Pockets (pepperoni flavor)

Displaying Files With the more Command

The more command is another way of looking at a file. It displays a file's contents one screen at a time, pausing after every screenful so that you can read each screen. To look at a file with more, type:

more filename

Once more has filled up the screen, you must give it a subcommand to tell it to continue. There are many such subcommands. Here are the most commonly used commands and their actions:

  • Spacebar: move forward one screenful
  • Return: move forward one line
  • b: move back one screenful
  • / string Return: search forward for string
  • q or Ctrl-c: quit
  • ?: help

more is clever enough not to display binary files and directories.

The more command is often used with a pipe to view commands that generate multiple screens of output. It is frequently referred to as a "pager" because it displays multiple "pages" (or screens) of information. Using a pipe, you can use more to display really long directory listings so you can view them page by page:

joeuser@athena:~$ ls | more

Copying a File (cp)

To make a copy tofile of an existing file fromfile, use the cp command:

cp fromfile tofile

If cp copies the file successfully, it returns you to the prompt. At this point, two identical copies of the file exist. The file specifications can be relative names or full pathnames. The destination can also be a directory instead of a file. In that case, the cp command will place a copy of the file in the directory in question. The following example demonstrates both cases. The first command will make a copy of the PARTY file and name it PARTY.backup. The second command will make a copy of the PARTY file and place it in the directory called Public:

joeuser@athena:~$ cp PARTY PARTY.backup
joeuser@athena:~$ cp PARTY Public/

Be careful: if a tofile file already exists with the name you specify, cp overwrites the file without asking you (This does not apply if tofile is a directory). To avoid this problem, use cp with the -i switch; in this case, the system asks you whether you really want to overwrite the existing file before it tries to copy. The original fromfile is not affected by the cp operation in any case.

Moving or Renaming a File (mv)

To move or rename a file, use the mv command:

mv fromfile tofile

The system renames fromfile as tofile, in effect moving it from one location to another (unlike the cp command, there is still only one version of the file when you use mv). Like cp, the tofile can be a file or directory:

joeuser@athena:~$ mv PARTY STUDYING
joeuser@athena:~$ mv PARTY Private/

Like cp, if a tofile file already exists with the name you specify, mv overwrites the file without asking you. To avoid this problem, use mv with the -i switch – in this case, the system asks you whether you really want to overwrite the existing file.

Whether or not mv renames the file successfully, it returns you to the Athena prompt.

Listing the Files in a Directory (ls)

The ls command lists a directory's contents. Suppose you are in your home directory. If you are a new Athena user, ls might return something like the following:

joeuser@athena:~$ ls

Mail OldFiles Private
Public welcome www

(Actually, the directory contains other files, but ls does not show the others because they are "dotfiles", files with names that are prefixed with a period.)

If you have had an Athena account for a while, you no doubt have other files and directories in your home directory, which would be listed by ls.

The ls command by itself lists just the filenames, alphabetically (A-Z before a-z) in as many columns as will fit across the screen. The ls command has many options. To see them all, use the man command to look at the online manual page for ls by typing man ls. This section discusses some of the more useful ones.

To get a list of all of the files in a directory, including those whose names begin with a . (dot) character, use the -a option (for "all"):

joeuser@athena:~$ ls -a

. .cshrc Mail OldFiles Private
.. .login Public welcome www

The file . always refers to the current directory, in this case your home directory /afs/ first-letter/ second-letter/ username. The file .. always refers to the current directory's parent directory, in this case your home directory's parent /afs/ first-letter/ second-letter. (See the section Working with Directories for more information about what these directory pathnames signify.)

To get a list of your files that shows more information about them, type ls -l:

joeuser@athena:~$ ls -l

drwx------ 2 joeuser mit 2048 Aug 18 17:00 Mail
drwx------ 2 joeuser mit 2048 Aug 18 17:00 OldFiles
drwx------ 2 joeuser mit 2048 Aug 18 17:00 Public
drwx------ 2 joeuser mit 2048 Aug 18 17:00 Private
-rwxr--r-- 1 joeuser mit 1915 Aug 18 17:00 welcome
drwx------ 2 joeuser mit 2048 Aug 18 17:00 www

The following table summarizes the parts of the ls -l output.

Element Example Definition
mode rw-r--r-- file's access permission modes
links 1 number of links the file has (for directories, this is how many subdirectories exist "beneath" the file, which is always at least two: itself and its parent).
owner jruser username of the user who owns the file (in most cases, your username).
group mit The name a group to which you can assign permissions (this doesn't apply to files in AFS)
size 1915 size of file in bytes (for text files, equals number of characters in file).
modify-time Aug 18 17:00 date and time when file was last modified (if file has never been modified, date file was created).
name welcome actual filename.

There are different types of files: simple files (text files, binary files, or shell scripts), and directory files. Often you need to know the type of the files you are listing. The -F option shows this information (this example shows a directory of someone who's used Athena for a while):

joeuser@athena:~$ ls -F

Mail/ OldFiles/ Private/ Public/
myprogram* welcome www/

Notice the suffix characters (/ and *) following some of the filenames. These characters are not part of the filename, but give information about the type of file:

  • (no suffix): regular file
  • /: directory
  • *: executable binary file or a shell script
  • @: symbolic link to another file
    As with many commands, you can combine ls options to use more than one at the same time. For example, to get a long listing of all the files in a directory, type ls -la.

Removing a File (delete and rm)

It is a good idea to delete files that you no longer need. This can help keep your directories from becoming too cluttered, and keep you from exceeding your allotted disk quota.

On Athena, there are two ways to get rid of unwanted files: delete and rm (remove). The delete command differs from the rm command in that delete is not necessarily permanent. When you use rm to remove a file, the file is erased from the system immediately and permanently; when you use delete to remove a file, the file is removed in such a way that you can recover the file (within about three days) before it is permanently eliminated from the system.

Completely erasing the file from the system is usually what you want, but once in a while you may accidently remove a file you wanted to keep – the manuscript for a paper that's due the next morning, for example, or part of your thesis! Because of this possibility, it is a good idea to use only the delete command; this helps you avoid mistakenly losing any files.

Using Delete and Related Commands

The commands that let you delete, recover, or remove files are summarized in the following table. (For more information about each command, including command-line switches, see the online man pages; for example, type man delete for details about the delete command.)

  • delete: Mark one or more files for permanent removal, making them invisible to the user (by renaming them with the prefix .#) but not actually erasing them from the system (use expunge or purge to permanently erase files marked for deletion).
  • undelete: Restore files marked for removal from current directory by delete (if not already expunged).
  • lsdel: List files marked for removal but not yet expunged.
  • expunge: Permanently remove specific files marked for removal.
  • purge: Permanently remove every file marked for removal in user's home directory and all subdirectories.

If you accidentally delete a file and then realize that you want it back, you can get it back by using undelete.

Because of the way delete works, deleting files does not actually lower the amount of quota you are using (each file is simply renamed to a form that is invisible to your normal work, specifically from filename to .#filename). To lower your used quota, you must fully remove the deleted files from your system by using the purge or expunge commands.

For example, suppose you have a directory containing the following files:

advisor notes thesis.tex thesis.tex~

Because you are near your quota, you decide to remove the old version of your manuscript file (the one ending with ~) to create some room. However, you accidentally leave off the ~ from your command and thereby remove the newer version of the file from the directory:

joeuser@athena:~$ delete thesis.tex
joeuser@athena:~$ ls
advisor notes thesis.tex~

If you had used rm to do this, you would not be able to recover the lost file, and would instead have to salvage what you could from the older file. However, because you used delete instead of rm, you can recover the deleted file by using undelete:

joeuser@athena:~$ lsdel
joeuser@athena:~$ undelete thesis.tex
joeuser@athena:~$ ls
advisor notes thesis.tex thesis.tex~

You can now remove the appropriate file, and even permanently eliminate it once you verify that you have marked the correct file for removal:

joeuser@athena:~$ delete thesis.tex~
joeuser@athena:~$ ls
advisor notes thesis.tex
joeuser@athena:~$ lsdel
joeuser@athena:~$ expunge thesis.tex~
joeuser@athena:~$ lsdel
joeuser@athena:~$ ls
advisor notes thesis.tex

Note that the undelete command only retrieves files removed with the delete command – it cannot retrieve files eliminated by rm. In addition, you cannot retrieve a deleted file that has been removed by purge or expunge. That is, you cannot undelete a file once it has been purged.

You can set up your system so that delete (rather than rm or rmdir) is automatically used whenever you want to remove files. Just put the following lines in the .cshrc.mine file in your home directory (which you can create if it does not exist):

alias rm delete -F
alias rmdir delete -D

Then when you type rm to get rid of a file or rmdir to get rid of a directory, delete is actually used.

Using the rm Command

The delete package is Athena-specific. The standard UNIX utility for removing files is rm, and it exists on Athena in addition to delete. (Athena recommends that you use delete rather than rm, since files that you rm accidentally usually cannot be recovered.)

To remove a file using the rm command, just type a command of the form:

rm filename

The rm command does not verify the deletion; it simply returns you to the joeuser@athena:~$ prompt. Because rm removes files permanently without confirmation, it is a very good idea to use the -i option with rm. The -i option stands for interactive; with this option, rm asks you to confirm the deletion you are performing.

Before you rm something, remember the old Unix adage: "rm is forever."

Summary of File/Directory Commands

The following commands let you list, examine, create, delete, copy, and rename files and directories:

  • ls: list contents of directory
  • cat: catenate and display file(s)
  • more: display contents of file one screenful at a time
  • tee: pipe copy of output into file
  • cp: copy file/directory
  • mv: move (rename) file
  • delete: mark file/directory for later permanent removal
  • expunge: permanently remove files marked for deletion
  • lsdel: list files marked for deletion
  • purge: permanently remove files under ~ marked for deletion
  • undelete: recover files marked for deletion but not yet removed
  • rm: permanently remove file
  • pwd: display name of current working directory
  • cd: change to the specified directory
  • mkdir: create new directory
  • rmdir: remove empty directory
  • echo: displays the typed text, expanding wildcards

IS&T Contributions

Documentation and information provided by IS&T staff members

Last Modified:

May 06, 2013

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