Intro to Scientific Computing PHYS 27/193 Physics Department University of the Pacific

CygWin

Cygwin is a set of unix-like components for MS Windows. Basically, you can set up a system which will have all of the basic (and many advanced features which we will explore) in a full fledged scientific computing environment under linux or solaris.

Getting Cygwin

Installing Cygwin is usually very easy. However, since Windows Vista was introduced, this is not always true. If you are using Windows XP, then you should be able to follow the outline below, starting from Installation. If you use Windows Vista then we will learn together what is best! There are various instructions on the web that I've found. Read this first:

Vista Pre-Installation Instructions

You can download Cygwin for free from the link below :

Download Cygwin setup.exe for windows

2. To install Cygwin click on setup.exe and Remember to Run setup as "Administrator" and with XP compatibility mode.

You will see Cygwin version that you are installing

3. Click next in Cygwin setup and select the root directory where you want to install Cygwin (C:\cygwin).

In Vista you need to select the install option: Just Me, because of Vista security, otherwise you will get errors afterwards.

XP and Vista

Below are the steps. The only slightly tricky part is picking the correct packages, which I'll discuss below.

The main cygwin site is: www.cygwin.com

Installation:

1. Download setup.exe.
   
   
2. Run the setup.exe application from your local harddrive.
   
   
3. Chose Next on first splash screen.
   
   
4. Select "Install from Internet" and click Next.
   
   



5. Enter preferred installation (so called: "root") directory and click Next.

   Unless you have good reasons for choosing otherwise, leave it as C:\cygwin. Also, take the defaults All Users and Unix File Types.
   
   




6. Enter a temporary installation directory. You can accept what it offers, which will put a folder on you Desktop. You can delete this folder later.

   So again, just click Next.
   
   




7. Select "Direct Connection" and click Next.
   
   



8. Select a download site and click next.
   (Any site that you can connect to is fine. Some sites are more stable and/or faster than others. Try to pick one that works for you. If one doesn't work, try another.)
   
   



9. Next you select the Packages you want to install. We will add to the default selections, a number of scientific tools and utilities.

   The Default Packages are already chosen.

   
   
   

   Notice that each package group (Accessibility, Admin, Archive, Audio, etc.)
   has a little [+] beside it.

   You want to install the following additional Packages, which you do by clicking the [+] sign before the Application Category, then click the word Skip in front of each Package listed below.
   When chosen, the word Skip will change to a number, which is the version of the particular package to be installed. In addition there will be a little box with an [x] in it.

   Note that you can stretch this window to make it bigger (and the packages more easily readable, by grabbing the corner with your mouse and click/dragging it.

   

   In each package group below, check these packages for installation::

   [+] Devel ->gcc-C ->gcc-C++ [+] Editors ->emacs ->emacs-X11 ->emacs-el ->vim [+] Graphics ->ImageMagic ->ghostscript ->ghostscript-base ->ghostscript-X11 ->gv ->jpeg ->libpng [+] Math ->gnuplot ->lapack ->octave [+] Net ->Openssh [+] Perl ->perl [+] Publishing ->tetex [+] Shells ->tcsh [+] Utils ->units [+] Web ->wget [+] X11 ->xorg-base ->xfig

   Please note sometimes you may get a download incomplete and the setup application will return to step 8. Simply select another server and continue the installation process.
   
   

   Installation may take several (tens of) minutes, depending on the speed of your computer and the connection to the cygwin mirror.

10. Once the installation is complete, click Finish.
    

Post Installation Notes:

Once you have installed the cygwin packages, we will configure your environment for use by following these steps.

1. Setup Windows HOME Environment Variable:
• Open your System Control Panel:
Select [Start]->Control Panel->System




• Select the "Environmental Variables" button under the "Advanced" tab of the "System Properties" Control Panel.
  
  



• In the Environmental variables window select the New button under the "User Variables" panel.
  
  
  
  Enter the new "User Variable" data as follows:
  Variable name: HOME
  Variable value: Path to where you want your home directory
  for example:   C:\cygwin\home\jhetrick

  Type in everything as shown above, except change my username (jhetrick) to your username.
  Your username is the name of your account, when you login to Windows. Hopefully it has no spaces in it (such as "John Smith").

• Next download and save the following two files to your computer. These are small scripts (programs) which will
  launch the X11 window server, and an xterm command shell.

  Save these two to your Desktop
  

  • mystartxwin.bat
  • launchxterm.bat

  
  g A Store this one in the folder C:\cygwin\home\YOURUSERNAME

  • .login

    If the folder C:\cygwin\home\YOURUSERNAME doesn't exist, save the file to your Desktop; we will make the folder later.
    (you can save these directly by right-clicking on the file, then chosing "Save Link As".))

  With this last file, .login, browsers seem to have a hard time. In Firefox, do the following:

  Save the file by right-clicking on the link. This will bring up the Save File dialog box:

  

  You need to change the following items

  

  to these: Change login.htm to .login and change Firefox Document to All Files

  

  Make sure the place you are saving to is your Home directory, as described above, then click Save.

  Before we use these files, let's review some terms introduced above.

  • X11 or Xwindows, from www.x.org
    From Wikipedia...
    In computing, the X Window System (commonly X11 or X) is a display protocol which provides windowing on bitmap displays. It provides the standard toolkit and protocol with which to build graphical user interfaces (GUIs) on most Unix-like operating systems and OpenVMS, and has been ported to all other contemporary general purpose operating systems.

    X provides the basic framework, or primitives, for building GUI environments: drawing and moving windows on the screen and interacting with a mouse and/or keyboard. X does not mandate the user interface individual client programs handle this. As such, the visual styling of X-based environments varies greatly; different programs may present radically different interfaces. X is not an integral part of the operating system; instead, it is built as an additional application layer on top of the operating system kernel.

    Unlike previous display protocols, X was specifically designed to be used over network connections rather than on an integral or attached display device. X features network transparency: the machine where an application program (the client application) runs can differ from the user's local machine (the display server).

    X originated at MIT in 1984. The current protocol version, X11, appeared in September 1987. The X.Org Foundation leads the X project, with the current reference implementation, X.org Server, available as free software under the MIT License and similar permissive licenses.^[1]

  • xterm short for X-Terminal. Back in the Day, we all sat at a Terminal--a computer looking much like a PC, and typed commands, like cp, mv, pwd, dir, sort, grep etc., which appeared on the screen at the prompt (something like this:  >). When we hit "Enter", the computer executed the typed commands. The X Terminal is a version of this which runs on a machine running an X server.

    A Terminal was just one connection into a large "Main Frame" computer, and many people at the site, lab, or company, had terminals on their desks. An xterm is a window which pops up on the screen, initializes itself, and gives you a prompt, meaning that it is awaiting commands from you.
    You can open many xterms on your desktop which giving you several terminals in which to issue commands.

  • A shell is just another name for the program that is interpreting the commands you type at the prompt.
    The shell accepts commands, starts programs, can dispatch them to run in the background, collect, sort, etc. the output, and return the prompt for more commands.

    Under Windows, you have only one choice of shell: the DOS shell.
    Under Unix, there are several shells, and unix users often come to like one shell over another. The reason is that each shell has strengths and limitations.
    All unix shells, however, recognize the basic unix commands such as (we'll learn more about these soon):

    • cp - copy files
    • mv - move and rename files
    • pwd - what directory am I in
    • rm - remove (delete) files
    • etc.

    Examples of commonly used shells are

    • the Bourne Shell (sh)
    • the C Shell (csh)
    • the Bourne Again Shell (bash)
    • the Technical C Shell (tcsh)
    • the Z Shell (zsh)
    • the Korn Shell (ksh)
    and several more.

    We will be using the tcsh since it is quite powerful and is the default shell on the SunRay system at Pacific.

  Playing with the DOS Shell

  If you are familiar with a Windows command window, an xterm is the unix version of the same thing.
  Just to remind ourselves what this is (and if you have never seen the DOS shell before, Do the following

  Click Start->Run on your computer, and in the box that pops up, type: command, and hit enter.

  A window should appear on your screen. This is an example of a DOS shell.

  The "prompt" is the string of characters ending with a" >" and a flashing "_" (underline).
  The DOS prompt has the current disk (C:) and folder, ending with the ">", like this:

  C:\Documents and Settings\jhetrick>_

  The prompt is where you type commands to the DOS shell.

  At the prompt, type dir. This gives a directory (or folder) listing of the current folder.
  In a unix shell, this command is ls. To see other DOS commands, type "help".

  
  
  

  Using the Startup Files

  These files are batch scripts, DOS commands stored in a file with the .bat extension. When you click on one of these, the system interprets and executes the commands as if you were in a DOS Shell. These will be the things you click to start up a Cygwin session.

  You should have stored put the two .bat files on your Desktop.

  To start the X-Windows server and open an xterm, double click on    mystartxwin.bat

  This should pop up a small DOS shell for a very short time, followed by a bigger window with a black background and an aquamarine text font, as shown below. This is a unix tcsh shell running in an xterm. Congratulations!

  

  
  

  ---

  If you DON'T have an xterm on your screen, or it doesn't look like the picture above, please email me and tell me what happens when you follow each of the steps above.

  ---

  
  The prompt in the xterm you just opened looks like this:

  XPS[~]|>

  (I have a Dell XPS laptop--your prompt should say something about your machine).
  The current folder (directory) is in this prompt as well; the "~" is shorthand for "your home directory. At the end is a pointer I've added: "|>".

  At this prompt, type

  ls -a

  You should see some files (several beginning with a ".") listed.

  
  Notice that in your taskbar, in the lower right corner, there is a small X.

  

  This means that the X-Windows server is running and unix applications can now open GUI (graphical user interface, i.e. mouse driven) windows on your desktop.

  Often you will want to have several xterms open on your desktop, doing something different in each one.
  To launch subsequent xterms, double click launchsxterm.bat.
  You DO NOT want to click mystartxwin.bat again, since this script starts the X server, which is only done once.

  Once the X-Windows server is running you can open as many xterms as you need.
  You do this by repeatedly clicking launchxterm.bat

  To illustrate this, close ALL of your xterms. You can do this either by killing the window it's in, or by typing exit at the prompt.

  Notice however, the X in your Task Bar indicating that the X-Windows server is still running. Closing your xterms doesn't shut this down. In fact, with the X server running, all you have to do to get a new xterm is double click launchxterm.bat. Try it.

  Now, if you click mystartxwin.bat while you have an already running X server, you will encur an error, even though the xterm does eventually pop up.

  To kill the X server, RIGHT-Click on the little X on your Task Bar, choose Exit, and click Exit again in the popup window.
  Now you should not see the little X in your Task Bar.

  Since you now don't have the X server running, launching an xterm should fail. You can verify this by clicking launchxterm.bat
  A DOS shell will popup momentarily, but then disappear.
  In order to get an xterm again, you have to restart the X server using mystartxwin.bat.

  
  Next: Test your Cygwin installation