More on Unix

Assignment :

Read the second chapter in your text book.

.Before proceeding to more Unix commands, it is important to review the basic commands for working with the file/directory structure. Make some test directories, and run ls to confirm that they are present.

More Useful Unix File System Commands

cp

make a copy of a file
Options

-i : inquire before copying a file over an existing file (existing file is lost)

Examples

"cp ~jhm/201/tutor.vi . " : copy the file "tutor.vi" from a subdirectory "201" located under jhm's home directory (jhm is a user login identifier), to the current directory ("." is a Unix abbreviation for current directory)
"cp ~jhm/201/tutor.vi ~ " : copy the file "tutor.vi" from a subdirectory "201" located under jhm's home directory (jhm is a user login identifier), to your home directory ("~" taken alone is a Unix abbreviation for your home directory)
"cp ~jhm/201/tutor.vi ~/my.vi " : copy the file "tutor.vi" from a subdirectory "201" located under jhm's home directory (jhm is a user login identifier), to your home directory giving it a new name of "my.vi"
"cp tutor.vi my.vi " : copy the file tutor.vi to a file in the same directory with the name "my.vi". This is a typical way to keep an untouched copy of a file around when you are about to make some changes.
"cp tutor.vi My-Stuff " : here I am assuming that a subdirectory called "My-Stuff" exists under the current directory. A copy of the file "tutor.vi" will by created in the subdirectory "My-Stuff".
"cp ../tutor.vi ." : you might use this command if you were in the subdirectory "My-Stuff and wanted to copy "tutor.vi" from the next directory level up (perhaps your home directory) into "My-Stuff".

mv

move a file to another location (rename a file)
Options

-i : inquire before moving a file over an existing file (existing file is lost)

Examples

"mv tutor.vi my.vi " : the file tutor.vi is given the new name "my.vi".
"mv tutor.vi My-Stuff " : here I am assuming that a subdirectory called "My- Stuff" exists under the current directory. The file "tutor.vi" will disappear from the current directory, but you will find it in the subdirectory "My-Stuff".
"mv tutor.vi My-Stuff/my.vi " : here I am assuming that a subdirectory called "My-Stuff" exists under the current directory. The file "tutor.vi" will disappear from the current directory, but you will find it in the subdirectory "My-Stuff" with the new name of "my.vi".
"mv ../tutor.vi ." : you might use this command if you were in the subdirectory "My-Stuff and wanted to move "tutor.vi" from the next directory level up (perhaps your home directory) into "My-Stuff", as part of a general reorganization of your files.

rm

remove (delete) a file that you no longer need. Be careful with this one. Unlike, Macs or MSDOS, there is no way to change your mind once you have told the system to remove the file.
Options

-r : stands for "recursive" and is only used if the name that follows is actually a subdirectory. This will remove the subdirectory including everything under it (files, lower levels of subdirectories and all of their contents. Use with extreme caution.

Examples

"rm tutor.vi " : remove the file "tutor.vi" from the current directory. .
"rm My-Stuff/my.vi ": remove the file "my.vi" from the a subdirectory called "My- Stuff"

rmdir

remove (delete) a subdirecory that you no longer need. Only works if you have emptied the subdirectory of all contents.

Examples

"rmdir My-Stuff ": remove the subdirectory named "My-Stuff"

Creating your own text files with the vi editor

This is how you will create your Fortran programs for this course. The most important thing you need to know about vi is that it operates in two modes, command and insert. When it first starts, it is in command mode. Any keys that you hit will be interpreted as commands to vi, not text to be inserted into the file. If one of the commands that you use is "I" or "a", you are placed into insert mode and subsequent characters are inserted into the current file. To return to command mode, you must hit the escape key (Esc). If you remember how to use "I" and "a" plus "x" (delete the character under the cursor) and "dd" (delete the line at the cursor), you will be able to survive with vi.

Knowing the basics of this editor is important, because it available on any Unix system that you use. You can walk into a new job, and start doing useful things immediately. I will teach the vi commands only by example in this course. You should rely on the homework and tutorials to get you started and polish your skills. If you have problems come to class help sessions.

Some Special Files in Unix

Any file name beginning with a "." is not displayed by "ls" unless you use the "-a" option. From your home directory (just type "cd" to get there), type "ls -a". You should see several files used by Unix utilities to store special default information. Two of these are:

.login

A file of commands that are executed every time you log into the machine. Often your path is set here.

.cshrc

A file of commands that are executed every time you start csh or tsch. This happens at login, or any time you open a new window in an Xwindows session. Your path might also be set or modified here. You might also see lines starting with "source" to run other files containing commands, or lines beginning "set" or "setenv" to set shell or environment variables serving as information sources to various utilities.

If you see a file ".alias" or ".aliases", look in ".cshrc" for "source .alias" or "source .aliases". If the appropriate "source" command is present, this alias file is run whenever ".cshrc" is, and by convention contains only "alias" commands. "alias" is the way you can make your own custom command definitions. To minimize my confusion switching between MSDOS and Unix, I keep some "alias" commands that translate DOS commands to the closest Unix command, and others that force the use of my favorite options. For example, my ".aliases" file contains the line:

alias dir 'ls -alF'

to mimic the look of the DOS "dir" command. I also include:

alias ls 'ls -F'

to distinguish between file names and subdirectory names, and between executable and non-executable files.

I'm nervous about inadvertently overwriting existing files so I also include

alias cp 'cp -i'

alias mv 'mv -i'

If the alias for "cp becomes an nuisance during a major housekeeping operation, I can always type

unalias cp

to remove my forced option.

File Redirection

Those of you familiar with recent versions of MSDOS may have used the concept of file redirection. There are times when you would prefer that a program's output to your screen be stored away in a file, either for future processing or so you can ignore it. This task is accomplished with combinations of the symbols ">", "!" and "&". For example the command

man ls > ls.doc

puts the manual pages for "ls" into a file ls.doc. If "ls.doc" already exists, this command will fail. However, if you want to overwrite any previous "ls.doc", you can type

man ls >! ls.doc

If you are building up a file with documentation from several commands, you can add more information onto the end of an existing file "command.doc" with

man ls >> command.doc

You may find these capabilities especially useful when compiling large programs with many errors. The command

f77 test.f >& compile.out

will capture all normal output plus special system error output (why "&" is used) in the file "compile.out".

Redirection can also be used for input. If I create a program called "myprog" that normally takes input from the keyboard, I can replace the keyboard input by lines from a file using "<"

myprog < input.file

One common use of this capability is to mail files to someone. If you want to mail the file "test.f" to me, just type

mail jhm@cac.psu.edu < test.f

Stopping programs

If a program appears not to be responding and you want to shut it down, you have several options. The first is to hold the control key and type "c" (usually denoted "^c" in documentation). This generally completely shuts down a job. The next option is to type "Control z". This suspends execution of the job. You can then completely eliminate it with the "kill" command. A third option is to use another window or login session to find the offending program with the "ps" command (generally you would use the -u option followed by your user ID). Once its job number is known, you can wipe it out with the "kill" command. Check man and/or Web tutorials for details on use of "ps" and "kill".

Suspending a program with "^z", also opens the option of continuing execution of the job in the "background" while you go on to run other commands. Right after typing "^z", type "bg", but be please note that if the program is scheduled to send output to your screen, this will continue, making whatever else you are trying to do confusing at best. You can also make a decision to run a program in the background when you first execute it. If I have a program called "hydro" that takes a long time to run and dumps all of its output directly to files, I might choose to type

hydro &

The ampersand at the end of the line sends execution of the job into the background while I am freed to type other commands. However, if I log off of the computer before "hydro" has finished running, Unix will normally kill the program prematurely.

Ending Your Interactive Computer Session

Recall that if you are working directly at a Unix Workstation in an Xwindows session you will need to position the cursor on the screen background, push the right mouse button, and follow the menu chain to log off of the machine. If you are connected to the Workstation via a telnet session, just type "exit". Watch for messages that indicate you are really disconnected from the machine. Sometimes you have forgotten that you are in some other relative of a shell session, and need to type "exit" again to really get off of the computer.

Review Questions

Test your knowledge with some review questions on this lecture.

Up one level / Home

Maintained by John Mahaffy : jhm@cac.psu.edu