1.1.1. Workstations

The Computer Science Department now consists of three general purpose labs on the third floor of Freedom Hall. All three labs contain Dell Optiplex AIO workstations that dual boot Windows 7®© and Slackware Linux. Room 303 has 24 machines, Room 308 has 20 machines and Room 322 has 22 machines. All 66 of these machines are running Intel core I7 processors running at around 3 GHz.

1.1.2. Servers

The lab has three servers: Stan, Vector-Sigma and Socrates. Stan is the Linux server and handles all mail, DNS lookups and our apache web server for the lab. Vector-Sigma handles all the Linux accounts. Socrates is a Linux machine that acts as the Windows server in our lab. It has come to be known as the "Winux" server. Since Linux is our primary operating system here in the lab, the Windows accounts are given as a privilege. In order to get a Windows account, you must be at least a sophomore and have a legitimate need for it.

1.1.3. The Cluster

The Computer Science Department now has a cluster built by Advanced Clustering Technologies containing 1 head node, 2 GPU nodes and 28 Compute nodes. There are over 1100 cores available that are used not only for learning parallel computing, but also run large data analysis on projects from other departments on campus including cancer and DNA research.

2.1.1. The Prompt

After entering your login name and password, you will be "logged in". You should see a tool bar and desktop window at the bottom, a mail box in the upper left hand corner, and a big Login Window. In the Big Login Window you should see the name of the machine followed by a :-) (smiley face). This is the prompt. After you click on this window with the mouse you can type in commands at the prompt.

2.1.2. The Password

The first thing you should do when you log into your account for the first time is to change the password from the random password given to you by your professor. You need to have a password that you can remember.

As a conscientious user, you should also make the security of your account a priority. Your password is your key to your account and only you should know it. To change your password, type the command yppasswd. First, you will be asked for your old password (type in current password) and then your new password (type in the new password that you wish to use). After your new password is typed, the computer will ask you for verification of the new password. Simply type in your new password again. If you happen to mistype the password in for the verification step, you will see a mismatch error and the computer will tell you that the password has not been changed. If you get a mismatch error, just begin again by typing yppasswd. Here is an example:

suzy:-) yppasswd

Changing NIS account information for ruth on cs.widener.edu.

Please enter old password:

Changing NIS password for ruth on cs.widener.edu.

Please enter new password:

Please retype new password:

The NIS password has been changed on cs.widener.edu.

Choosing a password should be done carefully. Your password should not be a word in a dictionary. It should have at least 6 characters. A mixture of upper and lower case characters and numerals is ideal. If you make your password too simple, someone using a password-cracking program can break into your account. Actually our system managers have such a program and will try to crack your password. If they succeed you will receive an e-mail message about it. Using numbers and mixed cases is strongly recommended for maximum security. An example of a good password is something like:

aPPles4Me

This password uses both uppercase letters and lowercase letters and a number making it hard for other people to discover. This type of password is also harder for people looking over your shoulder to figure out what you are typing in.

2.2.1. Listing files

Now that you know how to move in and out of directories, let us discuss the command to see what files are in the current directory. The command

ls for "list files and directories"

does this. For example if we are in the /home/IBM_Docs directory, then here is how ls would look:

The ls command sometimes does not list every file, especially in your home directory. Files starting with a . (dot) will not show up using just ls. In these cases, ls -al is needed. The -al is called a switch, which we discuss in more detail later. This command will allow you to see every file, the owner of the file, the group the file belongs to, the size, and the permissions on the file. Permissions will be discussed in more detail later on in this chapter.

2.2.2. Making Directories

You might want to start organizing and putting files into directories of your own. To make a directory, you type mkdir <directory name>. For example:

mkdir programs

2.2.3. Displaying files

To see the contents of a particular text file, you can type less filename. Fore example, after typing ls and noting the presence of a grades file, you might be curious to see what this file contains. To view this file for example you would enter:

less grades

CSCI 151 A

MATH 140 B

PHIL 120 C

CSCI 188 A

SOC 101 A

To exit out of less type q to quit. less allows you to scroll up and down your file with the arrow keys. One of the good features of less is that even if you use it on a binary file, no harm will result. It even shows you the hex codes of the unprintable characters.

2.2.4. Moving files

Once you start using your account, you will want to make directories and files to keep everything in order. A few commands that might be useful are described below.

If you have made a directory, you will probably want to move some files into it. To move files into a specified area, you type

mv <file> <destination>

For example, if you wanted to move the file firstprogram.py into the programs directory, you would type:

mv firstprogram.py programs

The command mv can also be used to rename files. To rename a file using the mv command, you type mv oldfilename newfilename. For example, if you wrote a program firstprogram and wanted to rename it numbers.py, you would type:

'''mv firstprogram numbers.py'''

The difference between moving a file and copying a file is that if you move it, a file with the old name no longer exists. However, if you copy it then two files (one with the old name and one with the new name) exists.

2.2.5. Copying files

You may also find it necessary sometimes to copy files. To copy a file, you type cp oldfilename newfilename. If you wanted to copy firstprogram.py into copy.py, you would type:

cp firstprogam.py copy.py

2.2.6. rm / rmdir

The last two basic commands that we will discuss are rm and rmdir. These commands allow you to remove (or delete) items. rm is used to remove a file. Rmdir is used to remove a directory. Follow the examples below:

'''rm junk.py'''

'''rmdir temp/'''

2.2.7. Printing Files

To print out a file you may enter print <filename> at the command prompt. For example:

print myprogram.c

This command is an alias which calls the lpr command. Occasionally, when printing from the web or from xpdf for example, you may need to enter this command. For example:

lpr -Pnetlaser -h myprogram.c

This will not work for binary files or files using an encoding the printer does not understand.

If you run into any problems printing, please don't hesitate to talk to a manager and they will help straighten out the problem.

2.2.8. USB Storage

To use a flash drive or other USB storage device, simply plug the device into one of the USB ports located on the front of the computer itself, or on the left hand side of the monitor. When you do this, you should see an icon appear on your desktop and the file manager will open showing you the contents of your drive.

To remove your flash drive from the system, right click on the desktop icon for your device and select Unmount Volume. You will then be able to remove your device from the system safely.

2.3.1. Common Unix Commands

2.3.2. Switches

You can only use rmdir on an empty directory. If the programs directory has files in it you can use the rm command like this:

'''rm -r programs'''

The -r identifier is called a switch. The -r switch tells the rm command to remove everything under programs including directories. Most UNIX commands can be modified by using switches. To see which switches work for a particular command use the man pages.

There are two good books on UNIX at the help desk: UNIX for Dummies by Levine and Young, and Using UNIX by Philip Laplante and Robert Martin.

2.3.3. Wild Cards

Suppose you wanted to save space in your directory, so you want to get rid of all files whose names end in “.o” (since these could always be reconstructed later). To get rid of them you could use a wild-card:

'''rm *.o'''

Suppose you have programs hello1.py, hello2.py, hello.py, and hellogoodbye.py and you want to get rid of them all. You might try:

'''rm hel*'''

However you might want to check if that you won't get rid of more than you want to by doing

'''ls hel*'''

If you had a program such as help.py, this would show up

2.4.1. Command Line

Suppose you decide that the only program that you want to get rid of is hello-goodbye.py and that you accidentally type:

'''rm hellogoodby.py'''

You will get the error: File not found. An easy fix is to use the up-arrow key to bring the misspelled line back and use the left arrow to go into the mistake and fix it. This is called command-line editing and is a feature of the shell. The shell is the command line interpreter. The shell given to the new users as well as to the system administrator is the “bash” shell (the Bourne again shell).

2.4.2. .bash_profile

The file .bash_profile allows users to customize their accounts. Users can change their default path, change their prompt, and even add aliases ( shortcuts to run specific commands). To add a directory to your path, add the directory you wish to add between the colons at the top of the profile.

In order to change the prompt, find the line that looks like this:

'''PS1 = h:-)'''

Now edit the text between the quotes. h is an escape character that will place the computers name in the prompt. Experiment to find a prompt you like.

To add or change aliases find the alias section. Aliases are formatted:

'''a shortcut = command'''

Make sure you study your bash profile before you edit it. And always make a back up before editing the original.

2.4.3. .forward

Users can forward their e-mail to another e-mail account. To do this just open your favorite editor and type the e-mail address you wish to have your mail forwarded to. Save the file as .forward in your home directory. Now when ever and e-mail comes to your computer science e-mail account it will automatically be forwarded to the account specified.

2.4.4. .bash_logout

The .bash_logout file is used to run commands when the user logs out of the system. To add commands to this file open it with your favorite editor and type the commands as a list in the file. Save the file and then log out. The script will be run automatically. A script has been developed to clean out temporary files that tend to accrue and clutter up your account. Please see a manager to have the script added to your .bash_logout file.

2.4.5. Files and Privacy

The files in your home directory belong to you. Whether or not other people can read them or use them is up to you. You can set permissions using the chmod command.

2.5.1. Emacs

Emacs is the most popular editor in Linux because it has graphical interface. Emacs also offers automatic spacing and indenting for programming languages like Lisp and C++.

2.5.2. Nano

Nano is a terminal style editor. There is no mouse interface face but nano's streamlined barebones interface is often preferred for script editing and remote access.

2.5.3. Libre Office

Open office is a Linux based program that can open and edit your windows office files. The interface is designed to mimic windows office in every detail. At the prompt enter soffice to start open office.

soffice

2.6.1. C/C++

C is a very powerful high level language. C++ is an object oriented programming language version of C. Both languages have a wide range of capabilities.

g++ <file.cpp> to call the C++ compiler

gcc <file.c> to call the C compiler

2.6.2. Cobol

Cobol is an older language that is still widely used in the business world. Many companies such as banks and credit card companies still have account software running on mainframes that was written in Cobol.

gcb <file.cob>

2.6.3. Java

Java is an object oriented programming language like C++ however java substitutes some of C++'s high end features for platform independence. While most languages compile into machine code for the system they are compiled on java compiles into byte code which is like machine code for the java virtual machine. So a java program complied on one machine will work on any computer with a java virtual machine. Because it is being reinterpreted ever time it is run, java programs run slower then other languages but platform independence is essential in environments like the internet where hardware varies so greatly from one machine to the next.

javac <file.java> Compile a java program

java <file> Run a java program

2.6.4. Lisp

Lisp is an early ("list processing") language. It is a functional language and relies heavily on recursion. Although it has many uses Lisp is most commonly used in AI programming.

2.6.5. Python

Python is a free, general purpose language available for almost every platform. It is very extendable and can suit almost any scripting or programming application due to the variety of modules available for it. It has an easy to read syntax that makes creating or modifying python programs easy. It has become a powerful language and is used in everything from search engines to office suites. To execute a python program enter:

python <file.py>

2.7.1. Browsers

Both the Linux network and the Windows network run Firefox as our primary browser. It is installed and ready to use on any computer in the lab by typing firefox at the prompt or double clicking the icons. NOTE: In Linux, new users will need to type the following command to launch firefox the first time:

run_firefox

After that it suffices to enter:

firefox

2.7.2. E-mail

There are two e-mail applications installed on every workstation for e-mail.

2.7.2.1 Pine

The options are pretty straightforward. To send an email message, you would want to type c to compose a message (send a message).

After hitting c you will see something like this:

2.7.2.2 ELM

Another mail reading program is called ELM, which stands for Electronic Mail. To run ELM, simply type elm at the prompt. The first time you run ELM, you will be asked if you would like a Mail directory made where all your mail will be placed. Answer yes to this question. After answering yes, you will be in ELM and ready to go. Here is an example of what you might see:

First, there is the ELM header. The next three lines indicate that there are three messages. Lastly, the bottom paragraph gives you a list of options. The options are pretty straight-forward.

To send a message, type m for mail. You will be prompted for the email address of the person you would like to send a message to. To send a message to someone locally on our system, you can use their login name. If your not sure what that is look in the /home/compsci directory.

Your email address here is your login name followed by @cs.widener.edu.

It looks like this:

loginname@cs.widener.edu

If you try to send a message to a bogus email address, your mail message will come back to you with an error saying "address unknown."

After you enter the recipient's name or email address, you will be asked for the subject of the message. You can enter anything you want here. Next, you will be asked if you wish to send copies (Cc) of this letter to anyone. After answering, you will be entered into the Emacs editor where you can type your message. Once you are finished and ready to send the message, hit ^XC (Control button then X then C). You will be asked if you wish to save the message, answer yes. Finally, you will be asked if you wish to send the message. Type s for send.

2.7.3. Your personal webpage

Every student at Widener is given their own space on our server to store whatever information they want. With this personal space you can hold many things including a folder that hosts your own personal webpage. Designing your own webpage can not only be a learning experience but it can also be very fun.

In order to start designing your own webpage you need to create a folder and change some permissions so your webpage can be displayed correctly. You can do this by entering your home directory. Your home directory is the directory that is named after your last name. If you are not sure what directory you're in try typing pwd (print working directory). To immediately enter your home directory you can type cd. That command will automatically take you to the home directory of the user you are logged in as.

Once you have entered your home directory you need to create a folder to hold your webpage files. Our web server, Apache, searches for directories named www. To create this directory, type mkdir www.

Once this directory is created you need to make sure the permissions on the directory are set correctly. If the permissions are not set correctly Apache may not have access to the folder and therefore cannot display your webpage. To change the permissions you must use a special command. We recommend using the permissions 755 for your www folder. To change the permissions make sure you're in your home directory and type chmod 755 www. If you are interested in learning more about permissions please check the Files and Privacy section of the lab manual.

Now you're ready to start creating your webpage. Make sure all your web files are stored somewhere inside this www directory. Apache, our web server, looks inside this directory when searching for your webpage and looks for a number of different pages. Your home page must be saved as one of these pages that Apache looks for. It searches for certain pages with the name index.html, home.html and home.php. Your home page must have one of these names or Apache will not know what webpage to load. Once your home page has one of these names other linked pages can be named whatever you want them too.

After you have the code for your home page written and stored in your www folder you can access it by going to the address

http://www.cs.widener.edu/~yourname. Let's say your login for your Linux account is smith. You can access your webpage by going to http://www.cs.widener.edu/~smith.

So as you can see setting up your own personal webpage is simple. Once you have set up your account the real challenge starts, making your webpage.

3.3.1. Office Suites

Every dual boot workstation has the Microsoft Office suite(Windows Network) and the LibreOffice suite(Linux Network) installed. LibreOffice can read and write almost all Microsoft Office files as well as files from other popular office suites, including the pdf format. It is also the first office suite to have complete compatibility with the open document standard format that will be required in the years to come.

4.3.1. Step One:

Enter ftp:// followed by the web address of one of the SSH Servers. In the example below the user is accessing Kenny.

4.3.2. Step Two

You will be prompted for a username and password. You must enter your computer science Linux username and password. Then click Login.

4.3.3. Step Three

After you click login you should be see a window that looks like the normal windows explorer interface. To download a file from the server simple cut or copy it to your local drive. To upload a file cut or copy it off of your local drives into the ftp window. Do not try to open and edit a file from this window. The interface is not step up to handle this type of action.

Alternatively you can use WinSCP to ftp into one of the ssh servers listed above. Using WinSCP to connect to a ssh server allows your ftp session to be encrypted and therefore provide more security for the systems and the users. Connecting to the secure ftp service with WinSCP is almost the same procedure as using regular ftp clients. If you need help accessing your account through ssh or through secure ftp, please ask the manager on duty and they will be glad to help you. WinSCP and Putty, which is used in the next section, are free and open source programs that can be found on the web or downloaded from our website.

http://www.cs.widener.edu/downloads

4.4.1 Initial Screen

This is the first Screen you should see.

4.4.2. Session Data

Enter the following data. Select SSH as the protocol. The port number should automatically change to Port 22. Then enter the web address of one of the SSH servers. The addresses are listed in the general remote access section. Finally pick an appropriate name for the session. Clicking save will add the session name to the list of saved sessions. Now this data can be recalled at anytime. It’s a good idea to add a session for each of the SSH servers. Now simple click open and an Xterm window will replace the current screen and prompt for a username and password.

4.4.3. Login

Login with your normal Linux password as you would in the lab. Remember that the username and password are cap sensitive.

4.4.4. Prompt

Once you hit this phase everything should be the same as when you are in the physical lab. Remember thought that unless to take the steps covered in the graphical remote access section graphical bases programs like Firefox and Emacs will not work through the prompt.