LINUX

These pages contain documentation of how to work in our LINUX environment. We hope you find all necessary information. Moreover, we hope that you inform us about all usefull suggestions to complete this documentation. Everything indicated with  is for advanced users, freshmen can skip these parts.

• Linux Operating System: General Information
• usefull information
• the KDE environment
• environment variables
• linux configuration
• login at the PC's of the 3rd floor
• work at home
• working with floppys
• Software
• Console Commands
• Scripts
• Interesting Links

About Linux

In the beginning a Un*x-like operating system may look much more difficult to use than other systems like MacO$ or M$ Windows. With a little patience you will discover that this not the case and the you can even do more with the same machine simply by using a good OS on it. But the following 'things' are confusing at first:

• Most if not all the command lines interpreters are case sensitive. This means that LS does not mean the same as ls. For M$ users this one of the strangest things and it get even more annoying when you know that filenames are also case sensitive. So be careful when you save something on disk.
• A command interpreter is called a shell under Un*x, not a prompt. It is also called a Console or Terminal.
• A Linux mouse has three buttons: the third middle button for copying and pasting. Select something to copy it, click the middle button for pasting (in a console or emacs). When your (Windows) mouse has only 2 buttons, you can do this by clicking both simulaneously.
• Each user has its own home directory. This is part of the security features provides by the OS. This means the other users can not remove your files and you can not remove theirs if the permissions are set correctly. All your files should be in your home directory, this is the only place where you have the permission to write, rename or delete files.
• There are no drives! Everything is a file. This uniform view has the advantage requiring no new command for accessing different drives. In fact you, as a normal user, can not see the difference between one drive and another. This drive can be a floppy, a hard disk but also network drive yet there is no difference. I mention this, but this is not really important for your PVM programming.
• M$ users watch it! Under Un*x the slash used to define a path to a file is the normal slash (/) not the back slash (\) like in M$ OS-es. In other words everything is like this: '/path/file' and not like this '\path\file'.
• What to do if you have a problem with a Un*x command? Easy, most of the commands have a so called man page (from manual page). This page describes the functions of the command and its different options. You just open a shell and type 'man xxx'.

Learn more about UNIX and linux

• Introduction to Unix (downloaded from here)
• chapter 3: learn the basics about the filesystem!!
• chapter 5: learn important UNIX basics like pipes, redirection, filters
• chapter 7: utilities (see also below: console commands)
• chapter 8: about shell scripts
• Linux Forum: a lot of info!
  
• manual on linux commands
  
• GNU manuals online
• advanced commands (like sed)
• For a good linux manual, look under emacs:
• select menu-item Help => Manuals => Browse Manuals With Info
• or CTRL-h-i (keep CTRL button down, press h followed by i)
• see under Miscellaneous
• move your cursor on a bold word and press ENTER to select it
• press 'u' for up, 'n' for next and 'p' for previous page

• Note that it is Single-click to start a program or file! To prevent a program or file to activate, keep the Control button pressed when you click. For example when you want to move or copy your file(s) to a different directory or you want to delete it. To select multiple files, also keep the Control button down.
• You have 4 desktops or workspaces, denoted by One, Two, Three & Four. A program is opened in the current desktop. They are efficient to organise your work. Just click them in the toolbar to change between them. Use a different desktop for each task you are doing (programming, internetting, experimenting, ...)
• Use Alt-TAB to change between windows in your workspace.
• The most important application are placed in the toolbar, more can be found under the big K (down left).

Environment Variables

• HOME or home : the pathname of your home directory .
• PATH or path: specifies the path that the shell searches when asked to execute a command. If an executable is not found in the path, you must specify its full pathname. Under Un*x you can only execute the file the are in your path. This path is stored in the PATH environment variable of every shell. So don't be surprised if you can see a file but you can not execute it even if you 'stand' in the same directory. There are two solutions to your problem:  give the full path to the executable on the command line or change your PATH environment variable. Ex: /home/my_self/a_directory_my_program
• USER or user: contains you login userid.

Linux configuration

• .cshrc: contains the definition of important environment variables

• in a console: use ls -all
• in the file manager: menu View => Show Hidden Files

Login at the PC's of the 3rd floor 

• login graphically with VNC (download executables: putty, VNCViewer)
• VNC under Mac
  

• Choose one among the following computers (use this IP-address when creating the tunnel with putty instead of localhost):

• Choose Port according to wanted resolution and color depth:

• Troubleshooting (known problems):
• Specify the tunnels correctly (see doc), don't forget to save your putty configuration.
• Too high resolutions are sometimes not accepted.
• Sometimes you'll better delete the xxx.rnd file in which putty stores your configuration.
  
• Check whether cluster computer is still 'alive'. Try an ssh node01  when connected with putty.
  

Work at home           For security reasons we don't put the correct addesses on the web, you'll have to ask us.

Work with Floppy's

mount /floppy

umount /floppy

• if mount /floppy doesn't work, consult the mount table (more /etc/fstab) and look for the entry with floppy and vfat, on some machines you have to mount /mnt/floppy
• you must be logged in on the machine you're working on

Software

• Console or terminal (in toolbar)
• see below for the most common Commands
• Add a terminal to your toolbar with a greater buffer:
• see below (configure desktop)
• put in the Execute line: /usr/bin/kvt -sl 512
• File manager Konqueror (in toolbar)
• Your personal files are under 'My Home'
• Use the right mouse click for folder and file operations
• Keep the Control key down to prevent the file to be started (remember that it is a Single-Click environment)
• Configure it
• set in the View menu item: Show Tree & Text View
• Push the Reload button to view the changements of the directory content
• a simple text editor Kedit (in toolbar)
• Mozilla: for browsing the net and reading your mail
• path: /usr/bin/netscape
• Kwrite or use the more professional Kate
  
• a simple file editor, with colouring of C++, html, xml, ... files
  
• F11: show Line Numbers
• Ctrl+I: Indent, Ctrl+Shift+I to Unindent (also when multiple lines are selected)
• Ctrl+D: Comment, Ctrl+Shift+D to Uncomment  (also when multiple lines are selected)
• Ctrl+B: Toggle bookmark on current line<>
• Alt+PageDown: go to next bookmark, Alt+PageUp: go to previous bookmark
• Emacs
• a powerfull editor, but less intuitive and Windows-style
  
• seperate documentation
• path: /usr/bin/emacs
• use Ksnapshot to make snapshots of screens
• look under Graphics => Snapshot
• use Kview to view images
• look under Graphics => Image Viewer
• use mpg123 or XMMS to listen to mp3 files
• for ftp and its commands, look here

1. Open the templates window (on your desktop). Drag the "Program" icon to your desktop, keep the Control button pressed & select copy!. It will be copied to the desktop.
2. Now you have a program link, to configure it, right-click on it and select "Properties"
3. Under the 'General' Tab, you can specify the name of the link (eg netscape.kdelnk)
4. under the 'Execute' Tab, you should specify the program you want to run (see higher for the right path). You can also select a different icon by clicking the icon.

Console Commands

• ls: list contents of directory
• ls -al: also show hidden files (start with a dot)
• lc: show all c++ files (makefile, c files, header files, ...)
• cd directoryname: change directory
• when you ommit the directory, you go to your home directory
• cd .. : go back to the parent directory
• cd ~: go to your home directory
• pwd: show the path of the current directory
• mkdir directoryname: create a directory
• ssh hostname: go to another machine (eg ssh info9) and work on that computer
• use exit to go back
• the first time you connect to that specific machine, answer yes when he asks for a secure connection and give your password.
• with hostname you get the name of the computer you are working on
• cp pathname-filename pathname: copy file to a different location
• ~/ is your home directory (eg cp mydoc.txt ~/docs/)
• mv pathname-filename pathname: move file to a different location
• nano filename: offers a simple command-line based text editor. Below you see the major commands, ^ means the ctrl key, eg. ctrl-x to quit, (it will ask for saving your file)
• use Control-c to stop a running program!!.
• use the Up & Down Keys to repeat commands (the command history)
• copy: just select a text, it is automatically copied to the clipboard
• paste: click on both mouse buttons at the same time
• TAB: to complete the name of a program, file or directory, press TAB again to get a list of all possibilities.
•    grep (look for a word in files), diff (compare 2 files for differences): see documentation
• ex:  grep -r "blabla" *    for recursive (search subdirectories) search of blabla in all files
• for counting the number of lines in which a word occurs:
• grep blabla <file> | wc -l
• wc = word count, -l option is for the number of line
  
• vi is a command-line based text editor, looks very strange if you are used to window-based editors
• edit file with vi file
• commands that should be typed on a line:
• i  to go in insert mode on that line
• Escape to quit this mode
• dd  delete current line
• commands:
• :w  save file
• :q  quit vi
• :q!  quit vi without saving the file
• archive your files with for example tar:
• create an archive (myfiles.tgz): tar -czvf myarchive.tgz *.*  (or multiple files, or in directories, like dir/*.*, etc)
• with the -z option, the archive is also compressed
• type tar --help for all options
• extract archive: tar -zxf myarchive.tgz 

Hints:

• use the TAB to complete incomplete directory and filenames (if you don't remember the full name of your file or you're just lazy)
• use the keys up & down to redo commands you typed before (very usefull!!)
• use the middle mouse button for copying, as explained here.
• for help about commands:
• command --help
• man command: consult the manual pages

Scripts

• C Shell:
• start script with line #!/bin/tcsh (tcsh instead of csh!!!)
• DO NOT FORGET: make it an executable with command: chmod +x myscript.csh
• doc or documentation or this (Unfortunately, not everything seems to apply for our system)
  
• check the examples:
• sed.csh: use sed to replace a string by another in a file
• sed_arg.csh: use program arguments
• files.csh: scans all files of a directory
• forallfiles.csh: runs a command of all files, and recursively on all directories
• convert_filenames.csh: convert all filenames of a directory to lower case names
• multiple_experiments.csh: run multiple experiments with different parameters
  
• $$ find out following scripts: check file extension, use special characters in grep & sed, replace windows-EOL with UNIX-EOL
• for calculations: @ y=$a + $b   (watch out for the spaces !!!)
  
• sh
• start script with line #!/bin/sh
• Good documentation with examples!
  
• Examples:

• fl.sh: remove all files from floppy and copy files from directory to floppy (very fast!)
• run.sh: run program mutiple times with different parameters
• crunch.sh: send commands to all machines

Linux Links

• Nederlandse LINUX-doc
• Newsgroups: comp.os.linux, be.comp.os.linux
• A LOT of LINUX links
• We support free software: The Open Technology Assembly, ww.gnu.org, www.gnu.be
• Windows emulators: www.vmware.com, www.winehq.com