Projects / Programming Assignments - CSCI 402, Spring 2018, All Sections

At the beginning of the semester, you are given a skeleton of an operating system with some of the lower-level machine specific parts filled in. In stages, during the course of the semester you are asked to fill in important missing pieces of various subsystems in the OS. The OS is based on the x86 architecture and should, in theory, compile to an image that can be run on a bare x86 machine. For simplicity, however, you will be testing and developing parts of the OS on an x86 emulator called Qemu.

The OS is written in C, so the programming assignments listed below assume familiarity with the C language. If you have not programmed in C before, we encourage you to pick it up on your own as quickly as possible before the semester starts.

You are allowed to do the kernel assignments in teams of 2 to 4 students (or you can do them by yourself). Please read carefully the section below on forming teams.

Warmup Assignments:

• Warmup Assignment 1 (doubly-linked circular list in C), due 11:45PM, 1/26/2018. Electronic submissions only.
• Warmup Assignment 2 (token bucket filter emulation in C), due 11:45PM, 2/16/2018. Electronic submissions only.

• GDB Assignment 1 (debugging Ubuntu Linux user space program)
• GDB Assignment 2 (debugging the weenix kernel)
• GDB Assignment 3 (debugging user space program running on weenix)

• Kernel Assignment 1 (processes and threads), due 11:45PM, 3/9/2018. Electronic submissions only.
• Kernel Assignment 2 (VFS layer), due 11:45PM, 4/6/2018. Electronic submissions only.
• Kernel Assignment 3 (virtual memory), due 11:45PM, 4/27/2018. Electronic submissions only.

Warmup 1:		7%
Warmup 2:		18%
Kernel 1:		25%
Kernel 2:		25%
Kernel 3:		25%

The warmup assignments must compile and run on nunki.usc.edu (which runs the Solaris OS).

Here is how team forming will work:

• You must decide on your project team for doing the kernel assignments before the end of day on 2/18/2018 (two days after warmup 2 is due). Each team member must send the instructor an email listing their team members (and copy all other team members on this e-mail). (It would be acceptable if one person would send such an e-mail to the instructor and copy to all team members and everyone else in the team just do reply-all and confirm that the information is correct.) Please only use USC e-mail addresses (and not gmail addresses).
• Once the team is formed and the kernel assignments started, the only way you can change your team is by mutually agreed swaps with another team. You can also break up the team if everyone in the team agrees to the breakup. Please keep the instructor informed if swaps or breakups are being done.
• All students not belonging to a group by the group forming deadline will be assigned a group by the instructor using a randomized algorithm (unless you have indicated that you want to do the kernel assignments by yourself) as follows:
  • form a list consisting only of these students then shuffle the list in a random order
  • assign 4 to a group starting from the beginning of the list
  • remaining students join these randomly formed groups
  • boundary conditions? Let's hope we won't get there.
  We know that this algorithm is far from perfect, that's why it is specified before the semester starts. This way, you can plan how to form teams given that you know our algorithm for assigning teams.

• More is not necessarily better: having more people on the team also increases the coordination overhead.
• In many teams, some of the contributors start to assume a passive role, leaving others to assume the larger burden of the work. To avoid this, you should have frequent team meetings, carefully delineated programming responsibilities, and internal deadlines that help ensure that everyone does their part on time.
• It's very risky to work with someone you don't know. You are strongly encourage to "work with" other students when you are doing the warmup assignments. "Work with" means to work together at a high level (i.e., not coding). When it comes time to write code for the warmup assignments, you must do it completely independently. This way, you can learn the habits of potential teammates.

We would like to encourage that everyone contributed equally to the team (or at least for you to declare as so in your README file). Therefore, your scores are maximized when you have an equal-share split. There may be penalty for not dividing the scores equally (i.e., for failing to work as a team). The actual equations we will you to determine the scores is a bit involved. The basic idea is to use "standard deviation" to measure how skew the amount of sharing is going on. When you have an equal-share split, the standard deviation is zero, that corresponds to an upper bound (i.e., no penalty). When you have a completely skewed distribution (e.g., 0/0/100 split), you would get the highest standard deviation and the most penalty. To make things easier to figure out, we have provided a program on nunki.usc.edu/aludra.usc.edu for you to run. The syntax is:

    ~csci551b/bin/cs402calc grade p1 p2 ...

    ~csci551b/bin/cs402calc 80 20 30 50

If the grader gave 80 points and the breakdown is 0/50/50%, you should run:

    ~csci551b/bin/cs402calc 80 0 50 50

If the grader gave 80 points and the breakdown is 0/0/100%, you should run:

    ~csci551b/bin/cs402calc 80 0 0 100

It's totally up to your team to decide how you want to assign the splits. If there are disagreements, the instructor will have to interview the team members (and ask questions such as, "What do this code do?") and make a decision.

Grade Normalization (for all programming assignments)

When I calculate your final class grade at the end of the semester, I will "normalize" each assignment grade according to the average and standard deviation for each grader and extrapolate your grade according to the overall class average and standard deviation. This "normalization" only applies to the grader-dependent part of your grade (i.e., without early/late submission extra credit and penalties and without class Google Group extra credit for kernel assignments. (If the overall score you get for an assignment is X, your early/late submission extra credit is Y percent, and your class Google Group extra credit for kernel assignments is Z, your grader-dependent part of the score is (X - Z) / ((100+Y)/100). After normalization of the grader-dependent part of your score, if your score is W, the score we will use to calculate your class grade would be W × ((100+Y)/100) + Z.) In the next two paragraphs, all the scores are grader-dependent part of your scores.

For example, if the average for a particular grader is 85 and standard deviation is 10 and you got a score of 87.5 (i.e., average plus half a standard deviation), your "normalized" score will be the overall class average plus half of the overall class standard deviation. This means that if you were graded by an "easy grader", your normalized score may be lower than your original score. If you were graded by a "harsh grader", your normalized score may be higher than your original score. This is not a perfect system. But I think it's a big improvement over not normalizing your scores and it's done this way so that you can have flexibility when you choose which section to enroll.

[BC: paragraph added 3/8/2018]
Since the purpose of grade normalization is to normalize the difference in grading among the graders. For a programming assignment, the highest possible normalized grade anyone can get is still the original maximum score assigned to that assignment, independent of the grader. Similarly, the lowest score one can get is 1 point given that an assignment was submitted for grading.

The following was by Pradeep Nayak, who took CS 402 in Fall 2012.

---------- Forwarded message ----------
From: Pradeep Nayak
Date: Thu, Oct 18, 2012 at 11:55 AM
Subject: [usc-cs402-f12: 822] Using Dropbox to manage and backup your code!
To: usc-cs402-f12@googlegroups.com

As professor mentioned in class, it's important to back up your code.I already use Dropbox for a lot of other things, hence using that as an example here. If you don't have a dropbox account, you can create one by using this link : http://db.tt/oLKgb3hw :-)

We will be using Dropbox to version control your code with git and also backing it up on Dropbox.

Things you need installed before you start:

1. You need git first! A simple way to install this would be sudo apt-get install git
2. Setup Dropbox for Ubuntu:https://www.dropbox.com/install?os=lnx. If you followed the default install procedure i.e (I agree to license terms -> Next ->.. Finish) you would be able to see a folder called Dropbox under /home//Dropbox where username is the current user you are logged in to the machine

Lets get started:

1. Set up a bare central repository on Dropbox. This is the place where you would be backing up your code along with version control

           cd ~/Dropbox
           mkdir kernel-project.git
           cd kernel-project.git
           git init --bare

2. Clone your remote repository on to your home directory. This is where you would be working on your project, committing changes etc.

           cd ~
           git clone ~/Dropbox/kernel-project.git

   You would now see a folder called kernel-project in your home directory.

3. Lets make the first commit:

           cd ~/kernel-project
           echo "Hello World" > foo.txt
           git add .
           git commit . -m "First Commit"

   Now you have committed the changes to your local repository. Next step is to push your code to Dropbox

4. Push code to Dropbox. Make sure you are in the kernel-project folder

           git push origin master

   So if your Dropbox is already running in background it would update your changes to Dropbox cloud. If not, the next time open Dropbox it would sync your changes on to the Dropbox servers.

Also, git is awesome to use when you are working on a collaborative project like this.

Useful resources:

• git cheat sheet
• Introduction to Git by Scott Chacon video
• Pro Git

Some people have reported problems with hosting their git repository on dropbox. The has two problems, one of them is more serious than the other

1. git runs garbage collection and updates its indexes every now and then. When dropbox is used, it may partially update an index and not other parts of the disk and any mistimed sync will cause damage to repo and loss of the index. This has seen been reported enough times that there is really no doubt that this does happen!
2. Unless people use different branches, or don't work on the files in the sames time. They are nullifying any collaboration going on.

BitBucket/GitHub is probably better than using DropBox because it combines version control and backup:

1. Create an academic account on BitBucket. You must use your USC e-mail address.

2. I do not recommend GitHub any more because a private repository automatically turns into a public one after two years (unless you pay). So, please do not use GitHub for this class.

3. You must make sure to make your git repository private. When you create a new repository, by default, the repository would be private. So, don't change that! If for some reason it's showing "public", select "private" before you create the repository). Failing to do so would be considered cheating (since you are allowing other students to cheat from you) and can lead to very serious consequences. If you cannot make your git repository private, you should NOT use BitBucket!

4. For a repository, you can change its settings and you can make the repository public. Please don't do that! If a prospective employer asks you to do that, you must tell them that you are not allowed to do that because you have agreed to the USC student conduct code when you were a student at USC and the USC student conduct code says that you must not cheat off other students and you must not knowingly allow other students to cheat off of you. You can e-mail them a private copy of your code and you must not include anything you do not have rights to distribute.

Once you have created a repository, say, "warmup1", you can do the following on your laptop in a terminal:

1. Change directory (using the "cd" command) to your "warmup1" directory then do the following only once:

       git init
       git remote add origin https://YOURACCOUNTNAME@bitbucket.org/billcheng/warmup1.git

2. Add files to the repository. For example:

       git add *.c *.h Makefile *README.txt
       git commit -m 'Initial commit'
       git push -u origin master --tags

3. After you have made changes to some of the files, you can do the following to update the repository:

       git commit -a
       git push origin master --tags

   You should do the above at least once a day so that what's on your laptop do not get too much out of sync with the repository.

The above are just some examples to get you started quickly. To learn more about "git", please please read the free online book, Pro Git, mentioned in the textbooks section of our course description web page.

1. The class programming assignments will be C code to be developed on a UNIX environment. No other programming language will be accepted and your program must compile and run with a Makefile as is. You must be familiar with the UNIX development environment (vi/pico/emacs, cc/gcc, make, etc.) Please read the general programming FAQ if you need a refresher on C file I/O and bit/byte manipulications.

2. For the warmup assignments, you should use your USC accounts and preferably work on the Solaris machines via ssh for testing. The final (submitted) program must run on nunki.usc.edu because we are going to test it in that environment. Please note that we can only grade your submission from the grading account on nunki.usc.edu. It would be a good idea to test your program in another student's account to make sure that it runs everywhere. By the way, you should not do the whole program development there, as nunki is a general purpose server - under heavy use by many students. But you should definitely test your program there. Please also note that regrades can only be done from the grading account on nunki.usc.edu.

3. For the warmup assignments, please do not hardcode any directory path in your code! If you hardcode something like "/home/scf-..." or "/auto/home/scf-..." in your code to access something in your home directory and the grader cannot access these directories during grading, we will not be able to make changes to the overall filesystem on nunki. You may only get a score of 1 point as a result of this. So, please make sure you are not doing this. All path should be specified externally, as far as your code is concerned.

   The only path that you can hardcode is probably "/tmp", and even that is not a great idea. What you can do is to define such a path as a compile time variable and pass it to your program. For example, you can use the following to define TMPDIR to be equal to "/tmp":

       gcc ... -DTMPDIR=\"/tmp\" ...

   Then in your code, you can do:

       char tmpfile[256];
   
       snprintf(tmpfile, sizeof(tmpfile), "%s/XXXXXX", TMPDIR);
       ... mkstemp(tmpfile) ...

   Basically, using a compile time variable is the same as doing the following in your code:

       #define TMPDIR "/tmp"

   The difference is that you are doing it outside of your code, and this is cleaner.

4. We will make grading guidelines available at least one week before an assignment is due. We will grade based on the grading guidelines (may be with minor adjustments). Since you know exactly how we are going to grade, grading will be harsh. The general rule is that you do not get credit for simply coding. You only get credit for getting your code to work correctly according to the spec and produce the correct output. (Please do not ask the grader to look at your code so you can get more points because you have done a lot of coding and your code looks like it should work. If your code is close to working correctly, it's your responsiblity to get your code to work correctly and produce the correct output.)

5. Late submissions will receive severe penalties. Please see the late policy.

6. All submissions will be timestamped by the submission server and receipts (known as tickets) will be issued. Whether your submission arrived to the server by the deadline is determined by the timestamp. Please do not delete your receipts/tickets from your home directory on nunki.usc.edu.

7. If you sign up late for this class, you are still required to turn in all the programming assignments on time or you will receive a score of zero for the applicable assignments. No exceptions! This requirement also applys to students on the wait list.

8. You must follow the Electronic Submission Guidelines when you submit programming assignments. Please note that this is a fairly new procedure and very different from previous procedures. Please make sure you read the output of the bsubmit program carefully. It should look similar to the sample output given on the bsubmit page. The timestamped upload ticket issued by the Bistro server is a proof that the server has received your submission (and you do not need additional proof such as an e-mail confirmation). You should also verify what you have submitted is what you intended to submit by following the Verify Your Submission procedure. Please note that it is your responsibility to ensure that you have submitted valid submissions and that you have received timestampted upload tickets for them. Please understand that a file system timestamp can be easily forged. The only kind of timestamp that we can accept is a timestamp given by a server under my control.

It should be clear that you cannot use code written by other students in a previous semester no matter what. As clearly in spelled out in the academic integrity policy of this class, if you have a copy of any of our programming assignments written by someone else, looking at the code or running the code is considered cheating, let alone copying code from it.

There are two exceptions to the above rule:

1. Code fragments done by yourself for another class or given to you as class resource in another class (which you have taken and completed) must be cited explicitly. Just mention that you got some code in another class in your README file is no good. You must surround such source code by the following comment blocks:

       /*
        * Begin code I did not write.
        * The code was given to the (class information) in
        *     (semester, year) at (institution name).
        * If the source code requires you to include copyright, put copyright here.
        */
       [ code you did not write yourself ]
       /*
        * End code I did not write.
        */

   If you decide to make changes to this type of source code, you should change the phrase "This code was given to ..." to "This code was derived from code that was given to ...".

2. You are allowed to use code given to you as part of this class (i.e., from textbook or lectures). You do not need to cite such code.

One line (128 characters max) of change is defined as one of the following:

• Add 1 line before (or after) line x of file y
• Delete line x of file y
• Replace line x of file y by 1 line
• Move line x of file z to before (or after) line y

Afterwards, additional modifications cost 12 points per line until 7 days past the submission deadline. After 7 days past the submission deadline, an additional modification costs 30 points per line.

Please note that this applies to source code, Makefile, and README files. Please understand that the grader is NOT allowed to modify your source code or Makefile during grading.

Just want to be very clear about this... The free 3 lines of changes are only applicable if you submit them within 24 hours of the submission deadline. Also, a "modification" is NOT considered a "new submission". So, sending a "modification request" will not change the timestamp of the submission we grade.

Chances are that you have corrupted memory (or have corrupted the memory allocation chain). Memory corruption means that a memory location got modified in a bad way and you have no idea when it happened or how it happened. It's as if it has gone bad all by itself. But since it really cannot go bad all by itself, it just be your code that somehow corrupted memory! When you notice that memory corruption has occurred, this usually implies that you have corrupted memory a while back. It just happened that when you call malloc() or free(), the corrupted memory caused a bus error or the execution of an illegal instruction. By the way, bus errors and illegal instructions are basically the same thing as segmentation faults. If you see something like "stack smash", it's another form of memory corruption bug (unless you really try to "smash the stack").

How does one corrupt memory (or corrupt the memory allocation chain)? You can write beyond an allocated memory block. You can free the same object twice. You can free an object that was not allocated. You can write to an object that's already freed. You can write to a portion of a stack space that is no longer valid. These bugs are hard to find because most of the them you only see that there is problem long time after you have "corrupted memory". We will talk about all this when we go over "dynamic storage allocation" in Ch 3 of the textbook.

If you have access to a professional/expensive debugging tool, it may be helpful. Otherwise, you just need to do binary search and see where the bug(s) might be. There's no magical cures in debugging memory corruption bugs, not even for professionals! I, unfortunately, do not have any magic tricks that can help anyone find memory corruption bugs.

One thing you might try is to temporarily turn off memory deallocation (if you suspect that you have freed the same object twice or freed an object that was not allocated). You can do the following to define free() as a no-op in a common header file when you are debugging:

    #ifdef DEBUGGING_MEMORY_CORRUPTION
    #ifdef free
    #undef free
    #endif /* free */
    #define free
    #endif /* DEBUGGING_MEMORY_CORRUPTION */

As your code gets more and more complicated, you may get more of these bugs. This is one reason why you want to keep your code nice and clean.

If you develop your code on a Linux machine, you can try valgrind. If you have installed Ubuntu 14.04 on your laptop/desktop, you should give it a try. Just prefix your commandline by "valgrind" (or "valgrind --tool=exp-sgcheck") and read the output carefully. Figure out why valgrind is complaining and fix EVERYTHING it's complaining about. Although valgrind cannot catch every memory corruption bug, it does a pretty good job. For warmup programs, it's worthwhile to make your code runs on both Linux and Solaris because you can use valgrind to look for bugs on Linux. This way, you won't have to look for all your bugs on Solaris which can be more painful!

If you have installed Ubuntu 14.04 on your laptop/desktop, just use the following command to install valgrind:

    sudo apt-get install valgrind

If your program is memory-corruption free and you just want to look for memory leaks, you can run your program by prefixing it with "valgrind --leak-check=full" and see what valgrind has found for you.

Recently, I have heard about two more memory debuggers.

• cppcheck - Static analysis of C/C++ code. Checks for: memory leaks, mismatching allocation-deallocation, buffer overrun, and many more. To install on Ubuntu, do

      sudo apt-get install cppcheck

• libefence - Helps you detect two common programming bugs: software that overruns the boundaries of a malloc() memory allocation and software that touches a memory allocation that has been released by free().

      sudo apt-get install electric-fence