Linux Lab

While you will be able to do subsequent labs on your Virtual Machine, you must complete this lab in the Computer Science Instructional Lab (CSIL).


  1. Become familiar with the Linux environment
  2. Learn basic terminal commands and how to work with a text editor
  3. Learn to run a Python program from the command-line
  4. Learn the basics of Git and chisubmit


Linux is an operating system much like OS X or Windows. It has windows, programs, web browsers etc. Files are stored in directories which, in turn, are stored in other directories. You can access all of these features by using your mouse and double clicking on icons. As we perform more and more complex tasks we find that interacting with the computer graphically using the mouse is ineffective. Linux allows us to interact with the computer entirely through text using a program called the terminal. (Macs provide a similar terminal application, and there are ways to use text-based commands on Windows too. But, Linux provides the lowest barrier to entry.) In this lab you will learn how to use the terminal to perform some basic operations in Linux. You will need these skills for the rest of the course.

We show many examples of sample output below. The output you see when you run the commands may vary a bit. For example, most of you are not named “Gustav Martin Larsson”.


On your personal computer, you probably navigate your hard drive by double clicking on icons. While convenient for simple tasks, this approach is limited. For example, imagine you wish to delete all of the music files over 5 MB that you haven’t listened to in over a year. This task is very hard to do with the standard double-click interface but is relatively simple using the terminal.

Click the Application button (at the top left) and type “terminal” in the input box. Click the “terminal” icon to open the terminal window. If you do not have a terminal icon, click the top-left icon and type in “Terminal” and hit enter.

A terminal window will open and you will see a string of the form:


where username has been replaced by your CNetID and computer is the name of the machine you happen to be using. This string is called the prompt. When you start typing, the characters you type will appear to the right of the $. The program that runs within a terminal window and processes the commands the you type is called a shell. We use bash, which is the default shell on most Linux distributions, but there are other popular shells, such as ksh, tcsh, etc.

The procedure for completing this lab is as follows. For each section, read through the explanatory text and the examples. Then, try these ideas by doing the exercises listed at the bottom of the section.

Show Files

The terminal will start in your home directory, /home/username/, which is a special directory assigned to your user account. No matter which computer you will use in the CSIL it will automatically connect to your home directory and all files that you created or changed in previous sessions in CSIL will be available to you.

Two very useful commands are pwd and ls:

pwd Prints your current Working Directory - tells you where you are in your directory tree.
ls Lists all the files in the current directory.

The following is an example using these two commands in a terminal window:

username@computer:~$ pwd
username@computer:~$ ls
Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos

Try these commands yourself and verify that everything looks similar.

Notice that the directory path and list of files that you see if you open your home folder graphically are identical to those provided by pwd and ls, respectively. The only differences are the way you obtained the information and how it is displayed.

Change Directory

cd <path-name> change to the directory path-name
cd .. move up/back one directory
cd move to your home directory

How can we move around in the file system? If we were using a graphical system we would double click on folders and occasionally click the “back” arrow. In order to change to a different directory in the terminal, we use cd (change directory) followed by the name of the destination directory. (A note about notation: we will use text inside angle brackets, such as <path-name> as a place holder. The text informally describes the type of value that should be supplied. In the case of <path-name>, the desired value is the path-name for a file. More about path-names later.) For example if we want to change to the Desktop directory, we type the following in the terminal:

cd Desktop

Here is an example of changing to the desktop directory in the terminal. We use pwd and ls to verify where we are and where we can go:

username@computer:~$ pwd
username@computer:~$ ls
Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos
username@computer:~$ cd Desktop
username@computer:~/Desktop$ pwd
username@computer:~/Desktop$ ls


Notice that after we cd into the Desktop the command pwd now prints out:


rather than:


In the beginning, there are no files in the Desktop directory, which is why the output of ls in this directory is empty.

We can move up one step in the directory tree (i.e. from /home/username/Desktop to /home/username or from /home/username to /home) by typing cd .. Here “up” is represented by “..” This command will move us up one level back to our home directory:

username@computer:~/Desktop$ pwd
username@computer:~/Desktop$ cd ..
username@computer:~$ pwd

Notice that the current working directory is also shown in the prompt string.

The tilde (~) directory is the same as your home directory: that is, ~ is shorthand for /home/username. Here’s another useful shorthand: a single dot (.) refers to the current directory.

Usually when you use cd, you will specify what is called a relative path, that is, you are telling the computer to take you to a directory where the location of the directory is described relative to the current directory. The only reason that the computer knows that we can cd to Desktop is because Desktop is a folder within the /home/username directory. But, if we use a / at the beginning of our path, we are specifying the path relative to the the “root” or top of the file system. For example:

username@computer:~$ pwd
username@computer:~$ cd /home/username/Desktop
username@computer:~/Desktop$ pwd
username@computer:~/Desktop$ cd /home/username
username@computer:~$ pwd

These commands achieve the same thing as the ones above: we cd into Desktop, a folder within our home directory, and then back to our home directory. Paths that start with a / are known as absolute paths.

Running cd without an argument will take you back to your home directory without regard to your current location in the file system. For example:

username@computer:~/Desktop$ cd
username@computer:~$ pwd

Setting up your CS121 directory

Before we practice these commands we need a set of files to practice on. Unfortunately your home directories are mostly empty. In this section we’re going to download a set of files for you to work with. We will do this using Git, a version control system and code-sharing tool. Git will be described in more depth later in the lab. For now please execute the following steps:

  • Make sure that your departmental Git account is correctly set up. Using a browser, go to and try logging in with your CNetID and password. When you type in your username, use only your CNetID username (without “”). If you are unable to log in, please speak with a TA.

  • Back in a terminal window, make sure that you are in your home directory /home/username

    using the pwd command. If you are not in that directory then use cd to change to it.

  • Run the following command in the terminal if you are on a CSIL computer:

    cs-setup-script cmsc12100-aut-17


Copy-Paste: In Windows (Mac) you usually copy-paste with Ctrl-C (Command-C) and Ctrl-V (Command-V). These short-cuts are available in graphical programs in Linux but not in the Terminal. Instead you can copy text just by selecting it with your mouse. Select the line that starts with cs-setup-script... above to copy it. You can paste by middle clicking where you would like it to go. Middle click in the terminal. You should also be able to use Ctrl-Shift-C and Ctrl-Shift-V, but you may find that this method does not work.

  • The setup script will ask you first to enter your CNetID:

    Enter your CNetID [username]:

    Where your CNetID will appear in place of username. You can either type in your CNetID, or hit enter to accept the username in brackets. Next, you will be asked for your CNetID password:

    Enter your CNetID password:

    Your password will be handled in a secure manner by the script, which simply needs it to access your information on the CS department’s Git server.


When you type in your password in a web browser, you may be accustomed to seeing an asterisk character appear for each character you type. This behavior is not replicated when typing passwords into the terminal: the password is not “echoed” back in any way (not even with asterisks) so don’t be alarmed if it looks as if you’re password isn’t being typed in.

  • Next, the script will print this:

    You are a member of the following repositories.
    Please select the one you want to use:
    [1] username
    [X] Exit
    Choose one:

    Just choose 1. Later in the quarter, you will become a member of other repositories as you work in groups with other students.

  • If successful, the script will print out the following:

    Setting up your Git repository...
    Your git repository has been created in /home/username/cmsc12100-aut-17-username
    Setting up chisubmit...
    chisubmit has been set up. You can use chisubmit commands inside /home/username/cmsc12100-aut-17-username

    Where, once again, your CNetID will appear in place of username.

    This output indicates that your Git repository has been correctly set up. The script also configured your CS121 directory for chisubmit, a tool you will use to submit your programming assignments. We’ll discuss chisubmit below.

  • After running the setup script, list the files in your home directory. You should see a new directory cmsc12100-aut-17-username. This directory will contain all of your work for this class. It contains a subdirectory, lab1, that has some files for us to play with. You will learn how to manipulate these files in the next section.

    Note that you will also see subdirectories named pa0, pa1. You can ignore these for now. Use pwd, ls, and cd to navigate to the lab1 subdirectory.

Using an editor

List the files in the lab1 directory. You should see the following:  test.txt

How do we view and edit the contents of these files? There are many high quality text editors for Linux. Today we will use Sublime Text, which is good for writing code.

You can open a specific file, say test.txt, using sublime-text (aka, subl) from the Linux command-line by typing:

sublime-text test.txt

or by typing:

subl test.txt

When you run either command,, you should get a new window showing the following text:

Author: Firstname Lastname

If the file is blank, quit sublime-text and ensure that the file test.txt exists in your local directory (use ls to list the files in your local directory). If it does not then use cd to navigate to the lab1 subdirectory inside the cmsc12100-aut-17-username directory.

For now, we will use sublime-text in a very basic way. You can navigate to a particular place in a file using the arrow keys and then type standard characters and use the delete key as you would in a regular text editor. You can save your changes using the save option in the file menu or better, use the keyboard shortcut Crtl-s. To quit, you can use the file menu quit option or the keyboard shortcut Ctrl-q.

As an aside, you can also launch sublime-text from the application launcher: simply click the Application button (at the top left of your screen), type “sublime-text” in the input box, and then hit enter. You can then use the file menu to navigate the correct file.


Make sure that you are comfortable with this level of usage by

  1. Adding your name after Author: in this file
  2. Saving the file
  3. Closing and reopening the file in sublime-text and ensuring that your name is still there.
  4. Finally, closing sublime-text.

Copy (cp) Move (mv) Remove (rm) and Make Directory (mkdir)

cp <source> <destination> copy the source file to the new destination
mv <source> <destination> move the source file to the new destination
rm <file> remove or delete a file
mkdir <directoryname> make a new empty directory

Sometimes it is useful to copy a file. To copy a file use the command:

cp <source> <destination>

where <source> is replaced by the name of the file you want to copy and <destination> is replaced with the desired name for the copy. An example of copying the file test.txt to copy.txt is below:

username@computer:~$ cp test.txt copy.txt

<destination> can also be replaced with a path to a directory. In this case, the copy will be stored in the specified directory and will have the same name as the source.


Try to accomplish the following tasks to practice and check your understanding of these terminal commands.

  1. Execute the above copy command and use ls to ensure that both files exist.

Move (mv) has exactly the same syntax but doesn’t keep the original file:

  1. Move the file copy.txt to the name copy2.txt. Use ls to verify that this command worked.

You can make a new directory with mkdir directoryname:

  1. Make a new directory named backups using the mkdir command.

Locations/paths can include directories:

  1. Copy the file copy2.txt to the backups directory.

You can list the files in a specific directory with ls directoryname:

  1. Verify that step (4) was successful by listing the files in the backups directory.

You can remove a file with the command rm filename:

  1. Now that we have a copy of test.txt in the backups directory we no longer need copy2.txt. Remove the file copy2.txt in this directory.

If you want to copy or remove an entire directory along with its the files, the normal cp and rm commands will not work. Use cp -r instead of cp or rm -r (the r stands for “recursive”) instead of rm to copy or remove directories:

  1. Remove the backups directory entirely using rm -r backups.

Make sure you want to remove everything in the named directory, including subdirectories, before you use rm -r.

Run a Python program

python3 runs the python program

In this class you will learn Python. To run a Python program, you just specify the command python3 and the name of the file that contains your program.

Use ls to verify that there there is a file named in your lab1 directory. Now run the program in by typing in:


This program is a very simple. It just prints “Hello, World!” to the screen.


There are several variants of Python, including Python 2.7 and Python 3. We will be using Python 3 and the corresponding python3 interpreter. The CSIL machines have Python 2.7 installed as the default Python. As a result, the command python runs a version of Python 2.7. There are some differences between the two languages and Python 3 programs may not run properly using a Python 2.7 interpreter.

Edit and run a Python program

In this section you will modify and rerun the program in This change is very simple but goes through all the mechanical steps necessary when programming.

You can open the file with the command:


The file contains a single line of code:

print("Hello, World!")

Change this line so that it instead says “Hello ” and then your name. For example if your name was Gustav Larsson the line would read:

print("Hello, Gustav!")

Do the following steps:

  1. Save the file in sublime-text (forgetting to save is a surprisingly common error)
  2. Rerun the program using python3

Let’s reinforce the steps to programming in Python with the terminal:

  1. Change your .py file with an editor
  2. Save the file
  3. Run with python3

Forgetting to save the file (step 2) is a very common mistake!


Git is a system used for developing software in a group. This system maintains files and all changes that are applied to them. You will each have a personal Git repository that is hosted on a central server. The server stores the project files and stores all changes to those files that have been uploaded to the repository.

We have created accounts and repositories for each of you on a CS department Git server. We will seed your repositories with templates and files that you need for labs and programming assignments. Also, we will be able to see any changes you upload to your repository, which allows us to provide help remotely, grade your programming assignments, and provide feedback.

Git tracks every version of a file or directory using commits. When you have made changes to one or more files, you can logically group those changes into a “commit” that gets added to your repository. You can think of commits as “checkpoints” in your work, representing the work you’ve done since the previous checkpoint. This mechanism makes it possible to look at and even revert to older versions of a file by going back to your code as it was when you “checkpointed” it with a commit.

When using Git, your basic working cycle will be:

  • Log into a CS machine (or your VM)
  • Change to your cmsc12100-aut-17-username directory
  • Download updates from the Git server (we will add files to your repository throughout the quarter). In Git, this operation is called pulling from the server.
  • Work on your files
  • Create a commit with any changes you have made
  • Upload the commit to the Git server. In Git, this operation is called pushing to the server.

The course staff does not have access to any files stored in your home directory or files that you have not pushed to the Git server. All we can access are files that have been pushed to the Git server, so remember to always push your latest commits when you’re done or when you ask a question on Piazza that will require us to look at your code.

Please navigate to your cmsc12100-aut-17-username/lab1 directory using cd. username should always be substituted by your CNetID.

Creating a commit

Creating a commit is a two-step process. First, you have to indicate what files you want to include in your commit. Let’s say we want to create a commit that only includes the file that you modified earlier. We can specify this operation explicitly using the git add command from the Linux command-line:

git add

There are various shortcuts that will allow you to add all of the files in a directory, such as git add . or git add --all. Using these commands is poor practice, because you can easily end up adding files that you did not intend. Instead, it is better to add files explicitly when you create them and then use the command from the Linux command-line:

git add -u

when you want to add any file that has changed since your last commit.

To create the commit, use the git commit command. This command will take all the files you added with git add and will bundle them into a commit:

git commit -m"Made some changes to"

The text after the -m is a short message that describes the changes you have made since your last commit. Common examples of commit messages might be “Finished part 1 of the homework” or “Finished lab 1”.


If you forget the -m"Comment" at the end then Git will think that you forgot to specify a commit message. It will graciously open up a default editor so that you can enter such a message. On the CS machines this editor is vim. To escape the vim view, press ZZ (shift-z twice). Now try git commit again and don’t forget the -m"Comment".

Once you run the above command, you will see something like the following output:

[master 99232df] Made some changes to
1 file changed, 1 insertion(+), 1 deletion(-)

You’ve created a commit, but you’re not done yet: you haven’t uploaded it to the server yet. Forgetting this step is actually a very common pitfall, so don’t forget to upload your changes. You must use the git push command for your changes to actually be uploaded to the Git server. If you don’t, the graders will not be able to see your code. Simply run the following command from the Linux command-line:

git push

You should see something like this output:

Counting objects: 7, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 452 bytes, done.
Total 4 (delta 1), reused 0 (delta 0)
   c8432e4..99232df  master -> master

You can ignore most of those messages. The important thing is to not see any warnings or error messages.

You can verify that our Git server correctly received your commit by visiting the following page:

Where username should be substituted by your CNetID.

This URL takes you to the web frontend of our Git server (please note that you will have to log in using your CNetID and password). More specifically, the above URL will show you the contents of your repository, exactly as it appears on the Git server. You can click on “Files” to see your repository’s files, and on “Commits” to see the latest commits uploaded to the server. If you see a commit titled “Made some changes to Hello World”, then your commit was successfully uploaded.

In general, if you’re concerned about whether the graders are seeing the right version of your code, you can just go to the above URL. Whatever is shown on that page is what the graders will see. If you wrote some code, and it doesn’t show up in the above URL, make sure you didn’t forget to add your files, create a commit, and push the most recent commit to the server.

Pulling changes from “upstream”

When we distribute new homework assignments or lab materials, we will do so through Git. These files are located in a separate repository on our Git server, which we call the “upstream” repository. The setup script you ran earlier already configured your Git repository so you can easily download any new files we upload to the upstream repository). To download these changes, run this command from inside the cmsc12100-aut-17-username directory:

git pull upstream master

If you run it now, nothing will actually happen, since we haven’t changed anything in “upstream” since the start of this lab. You should see something like this output:

 * branch            master     -> FETCH_HEAD
Already up-to-date.

When you pull from “upstream”, Git automatically downloads any new files or changes that have been committed to “upstream” and updates the files in your repository. If you have made local changes to files that have changed upstream, Git will attempt to merge these changes.

After you’ve pulled from upstream, any new files or changes will only be downloaded to your local copy of cmsc12100-aut-17-username. As with any other changes to your code, you need to run git push to upload them to the Git server (you don’t need to do a git commit to prepare a commit, though; git pull already takes care of this task).

  • Every time you work on your code, you should run git pull upstream master in your cmsc12100-aut-17-username directory before you do anything else. Sometimes, the instructors notice typos or errors in the code provided for a programming assignment, and they’ll commit fixes to upstream. By running git pull upstream master, you can make sure that those fixes propagate to your code too.

Pulling your changes from the server

If you have done work and committed it to the server from a lab computer and now wish to work on your VM (or vice versa), you will need to pull these changes from the server to your VM. To download these changes, run this command from inside the cmsc12100-aut-17-username directory:

git pull

It is important that you commit your changes after every session and that you pull from both upstream and cmsc12100-aut-17-username before you start to do any work.


Your output may vary from our sample output slightly. Do not worry about the difference unless you see an error message or a warning message.

git add revisited and git status

So far, we’ve created a single commit with a single file that we had already supplied in the lab1 directory. If you create new files, Git will not consider them a part of the repository. You need to add them to your repository explicitly. For example, let’s create a copy of


Is part of your repository? You can use the following command to ask Git for a summary of the files it is tracking:

git status

This command should output something like this:

# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#   modified:   test.txt
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
no changes added to commit (use "git add" and/or "git commit -a")

The exact output may vary depending on how far along you got in previous sections of the lab. However, the important thing is that there are two types of files listed here:

  • Changes not staged for commit: This is a list of files that Git knows about and have been modified since your last commit, but which have not been added (with git add).

  • Untracked files: This is a list of files that Git has found in the same directory as your repository, but which Git isn’t keeping track of.

    You may see some automatically generated files in your Untracked files section. Files that start with a pound sign (#) or end with a tilde should not be added to your repository. Files that end with a tilde are backup files created by some editors that are intended to help you restore your files if your computer crashes. In general, files that are automatically generated should not be committed to your repository. Other people should be able to generate their own versions, if necessary.

To add a previously untracked file to your repository, you can just use git add (unlike the previous commands, don’t actually run this just yet; you will be doing a similar exercise later on):

git add

If you re-ran git status you would see something like this:

# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#   new file:
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#   modified:   test.txt

Notice how there is now a new category of files: Changes to be committed. Adding not only added the file to your repository, it also staged it into the next commit (which, remember, won’t happen until you actually run git commit).

The git status command reports the status on the local copy of the full repository. If you wish to look at the status of a smaller part of the repository (the directory you are working in for example), you can add a path name to the status command. For example:

git status .

reports the status of the current directory (a single dot is the path used to refer to the current directory).

Unstaging, discarding changes, and removing files (optional, skip if short on time)

Take a closer look at the git status output above. Git is providing you hints in case you want to undo some of your work.

For example, you can use git reset to unstage the file. Doing so reverses git add so you can create a commit only of changes to other files. This is good practice if you think the changes you made to don’t logically go in the commit you are going to make.

Another useful git command is git checkout. This command will undo modifications to files. If you again look at the above git status output, you will see in the last line that test.txt was modified. To undo any changes to the file, type git checkout test.txt. This command will revert the file content to match the last commit you made in your repository’s history

Finally, if you would like to remove a file from your directory, using git rm test.txt combines the result of doing rm test.txt and git add test.txt.

Looking at the commits log (optional, skip if short on time)

Once you have made multiple commits, you can see these commits, their dates, commit messages, author, and an SHA-1 hash by typing git log. This command will open a scrollable interface (using the up/down arrow keys) that you can get out of by hitting q.


  1. You have already changed the test.txt file in your directory. Verify this by using the command git status. You should see it under Changes not staged for commit.
  2. Use git add and git commit to create a commit that includes only the test.txt file. A good commit message would be “Added my name as Author in test.txt”.
  3. Upload your work to the server using git push.
  4. Verify that this file was sent by again using the command git status. You should see that the file test.txt is no longer listed.
  5. If you have not already done so, use cp to make a copy of named
  6. If you run git status, should show up under Untracked files. Add it to the repository using git add.
  7. Run git status again. Is in a different category of files now?
  8. Although we have added this file, we have not yet created a commit. Create a commit and push it to the server.
  9. Run git status a final time to verify that was committed (if so, you should not see it in any category of files)
  10. Run git push to upload your changes to the server.

We strongly recommend you to check in and push changed files as often as possible, especially if you finished some work and are about to log off a computer. This way the latest files are accessible from any other computer where your repository is set up.


You will be using a locally-developed system named chisubmit to submit your programming assignments. The set-up script that you ran earlier set you up to use chisubmit in addition to initializing your Git repository.

All chisubmit commands should be run from within your cmsc12100-aut-17-username directory.

chisubmit has commands for managing assignments. Here are descriptions and sample runs of some of the more useful commands. You can run these commands as you read through this section.

chisubmit student assignment list: lists upcoming programming assignments and their deadlines.

username@CS-Vbox:~/cmsc12100-aut-17-larsson$ chisubmit student assignment list

pa0 2017-10-06 16:00:00-05:00   Programming Assignment 0

chisubmit student assignment show-deadline <assignment name>: lists deadline information for the specified programming assignment.

username@CS-Vbox:~/cmsc12100-aut-17-larsson$ chisubmit student assignment show-deadline pa0
Programming Assignment 0

     Now: 2017-08-26 12:32:19-05:00
Deadline: 2017-10-06 16:00:00-05:00

The deadline has not yet passed
You have 41 days, 3 hours, 27 minutes, 41 seconds left

chisubmit student assignment register <assignment name>: registers a student for a specific assignment. You will do this step once per assignment.

username@CS-Vbox:~/cmsc12100-aut-17-larsson$ chisubmit student assignment register pa0
Your registration for pa0 (Programming Assignment 0) is complete.

chisubmit student assignment submit pa0: submits your current commit

username@CS-Vbox:~/cmsc12100-aut-17-larsson$ chisubmit student assignment submit pa0

SUBMISSION FOR ASSIGNMENT pa0 (Programming Assignment 0)

This is an INDIVIDUAL submission for Gustav Martin Larsson

The latest commit in your repository is the following:

     Commit: eeed8efa66a13c0b04c587acdda43fbe75c9b99b
       Date: 2017-08-26 13:47:16-05:00
    Message: Added log for testing purposes
     Author: Gustav Martin Larsson <>


You currently have 0 extensions

You are going to use 0 extensions on this submission.

You will have 0 extensions left after this submission.

Are you sure you want to continue? (y/n):  y

Your submission has been completed.

chisubmit has many other commands, including command for canceling registrations, canceling submissions etc. You can find detailed instructions on these and other commands here.

Pulling on another machine (optional, skip if short on time)

Now let’s return to Git. This part requires that you have a laptop with you and that you have gone through the process of setting-up your laptop with the CS121 VM and with your CS121 repository. If you do not have a laptop or do not have one with you, you can just skip this this section.

If you look at your files in lab1 on your VM, you’ll notice that they are out of date. The changes you made to test.txt are not visible and, the new file you added earlier, is missing. Why? Because your local copy on your VM is out of sync with the authoritative version of repository on the server.

Run git pull from the Linux command-line to pick up your changes. Once you run this command the file test.txt should have changed and there should be a file named

As long as you committed and pushed all your changes on the CSIL machines to the server, the copies of your repository on the CSIL/CS machines, your VM, and the server will be the same.

Merge conflicts (optional, skip if short on time)

The beauty of Git specifically, and version control in general, is that you can share repositories with other people and you can work on the code separately. Merge conflicts arise when different copies of the repository get changed in incompatible ways. Unfortunately, this complication can arise even if you are the only one working on your repository! You just need to work on your code using multiple machines.

Let’s work through an example. Let’s say I take the following steps using a CSIL machine:

  1. Change the line in from:
print("Hello, World!")


print("Hello, Chicago!")
  1. Add and commit these changes.
  2. Forget to do a push.

And then switch to my VM and do the following:

  1. Run git pull inside my cs121 directory to pick up the most recent copy from the server.
  2. Change the line in from:
print("Hello, World!")


print("Hello, New York!")

(Notice that the change from “World” to “Chicago” did not make it to my VM because I forgot to push!)

  1. Add, commit, and push these changes to the server.

And then, finally, switch back to my CSIL machine and run git pull to pick up the most recent version from the server. This command will fail with an error like the following:

username@CS-Vbox:~/cmsc12100-aut-17-larsson/lab1$ git pull
remote: Counting objects: 4, done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 4 (delta 1), reused 0 (delta 0)
Unpacking objects: 100% (4/4), done.
   62c72de..b70ae2a  master     -> origin/master
Auto-merging lab1/
CONFLICT (content): Merge conflict in lab1/
Automatic merge failed; fix conflicts and then commit the result.

Git was not able to reconcile my local changes with the version on the server automatically and so, it updates to reflect the conflicts. The file will look like this:

<<<<<<< HEAD
print("Hello, Chicago!")
print("Hello, New York!")
>>>>>>> b70ae2a739c7775189b284be04ae568568ac3c62

The lines between <<<<<<< HEAD and ======= contain the code as it exists on the CSIL machine, where as the lines between ======= through >>>>>>> b70ae2a739c7775189b284be04ae568568ac3c62 contain the code from the server. In general, a failed merge can yield a mix of merged and unmerged blocks. I will need to resolve these conflicts by choosing among the offending lines and removing the conflict markers (<<<<<<< HEAD, =======, and >>>>>>> b70ae2a739c7775189b284be04ae568568ac3c62). And then I’ll need to add, commit, and push the updated files, before I can pull or push my code successfully.

Remote Access (optional, skip if short on time)

We’ll finish up with a description of some useful commands. If you run out of time, you can skip this part and return to it later.

There are two main tools for accessing a remote computer through the command line: one for running commands on the remote computer, and one for file transfer. The first of these commands is much more likely to be useful in this class.


SSH allows you to open a terminal session on a computer remotely, and is a major motivation for becoming proficient with the terminal. The following command:

username@computer:~$ ssh username@domain

begins an SSH session, and allows you to access all of your files and programs on the remote computer (as long as these programs can be executed through the shell). The command for SSHing into CSIL Linux computers is:

username@computer:~$ ssh

You should try this now and ask a question if you have trouble, as it is something you may have to do for your CS classes here.

To exit an SSH session, simply use the command exit.

ssh is installed by default on Linux and OSX. PuTTY is a popular SSH client for Windows.


While SSH allows you to log in to another computer, SCP provides the ability to transfer files between computers. In general, SCP is called as:

username@computer:~$ scp user@host1:/path/to/file1 user@host2:path/to/file2

and copies a file from one computer (the first argument) and places it in the second computer (the second argument).

If you want to copy a file to your local computer, you can simply specify the second argument as a file path, without the username or domain name; the same principle applies for copying from your local computer.

If you want to leave the file named as it was, you don’t need to specify the file name in the second argument.

An example of using SCP would be:

username@computer:~$ ls
Desktop Downloads
username@computer:~$ scp .
username@computer:~$ ls
Desktop Downloads Grade.txt

Recall that a single dot (.) refers to the current directory.

scp is useful, but do not use it to move files in your cmsc12100-aut-17 repository between machines. It is much safer to use Git to manage the files in your repository.

Final Notes

Sometimes, a program will run indefinitely or misbehave. When this happens, you can type Ctrl+C to send an interrupt signal to the running program, which usually causes it to terminate. On occasion, you may need to type Ctrl-C a few times. Typing Ctrl+D sends an end of input signal, which tells the program that no more information is coming.