Project II- s a set of files

CS214 
Project II


1 Summary
Write a program that analyzes a set of files and reports their similarity using the method described
below. Your program will use two or more threads to read directory entries and analyze the word
frequencies of text files, then compute the Jensen-Shannon distance between the word frequencies of
pairs of files.
2 User interface
Your program will be given the names of one or more files and directories, and up to four optional
arguments specifying program parameters. The file names and directories are used to determine
the set of files to analyze. File names given as arguments are added directly to the set of files. For
each directory, your program will add any files whose names have a particular suffix to the set, and
recursively traverse any subdirectories.
For each (unordered) pair of files in the analysis set, your program will output the Jensen-Shannon
distance between their word frequencies.
For example:
$ ls bar
baz.txt quux spam/
$ ls bar/spam
eggs.txt bacon.c
$ ./compare foo bar
0.03000 foo bar/baz.txt
0.12000 foo bar/spam/eggs.txt
0.80000 bar/baz.txt bar/spam/eggs.txt
1
Table 1: Parameters specified by options
Parameter Option Argument Type Default
Directory threads -dN Positive integer 1
File threads -fN Positive integer 1
Analysis threads -aN Positive integer 1
File name suffix -sS String ".txt"
In this example, the arguments are foo (a file) and bar (a directory). One file in bar matches
the default suffix (".txt") and is added to the file set. The subdirectory bar/spam is also traversed,
and its files that end with the suffix are added. This results in the file set foo, bar/baz.txt, and
bar/spam/eggs.txt. (Note that foo does not need to end with the suffix, because it was explicitly
given by the user.)
For each pair of files in the file set, the program outputs the JSD and the (path) names of the
files being compared. Comparisons are printed in decreasing order of combined word count (that is,
the total number of words in both files). Note that pairs are unordered, so the output will include
comparisons of foo and bar/baz.txt or bar/baz.txt and foo, but not both.
2.1 Regular arguments
Your program will take one or more regular arguments, which must be the name (or a path to) a
file or directory.
Each file name is added to the set of files to examine.
Each directory name is added to the set of directories to traverse. For each directory in the set,
your program will read through its entries. Any file whose name ends with the file name suffix is
added to the set of files to examine. Any directory is added to the set of directories to traverse.
Entries that are not directories and that do not end with the specified suffix are ignored.
Exception Any entry in a directory whose name begins with a period is ignored.
2.2 Optional arguments
Your program takes up to four optional arguments, which are used to set program parameters. For
simplicity, we will assume any argument that begins with a dash (-) specifies an option. The first
character following the dash indicates which parameter is being specified, and the remainder of the
argument gives the value for that parameter. Table 1 gives the syntax for the four options, and the
default values for the parameters of the options are omitted.
For simplicity, you may require all optional arguments to occur before the regular arguments
in the argument list, or allow them to be intermixed. You may require that an optional argument
occur at most once, or allow later arguments to override earlier ones.
You must allow options to be given in any order.
Your program must detect any invalid optional arguments and halt with an error message.
Possible errors are an invalid option (e.g., -x), or an invalid or missing argument (e.g., -f0 or -d).
Note The file name suffix may be an empty string, which would be indicated by the option -s.
2
Table 2: Word frequency distribution example
Text: I can’t understand thieves’ cant.
Word Occurrences Frequency
cant 2 0.4
i 1 0.2
thieves 1 0.2
understand 1 0.2
3 Operation
Your program will compute the word frequency distribution for each file in a set of files. For each
pair of files in this set, it will compute the Jensen-Shannon distance (JSD) between the distributions
for those files
3.1 Word frequency distribution (WFD)
The frequency of a word is the number of times the word appears divided by the total number of
words. For example, in the text “spam eggs bacon spam”, the frequency of “spam” is 0.5, and the
frequencies of “eggs” and “bacon” are both 0.25.
The word frequency distribution (WFD) for a file is a list of every word that occurs at least once
in the file, along with its frequency. Ignoring rounding errors, the frequencies for all the words will
add up to 1.
Tokenizing To compute the WFD for a file, your program must read the file and determine what
words it contains. For this project, we define a word to be a sequence of word characters, where word
characters include letters, numbers, and the dash (hyphen). Words are separated by whitespace
characters. Other characters, such as punctuation, are ignored.
To compute the WFD, keep a list of every word found in the file and its count. Each time a
word is encountered, look for it in the list and increment its count or add it with count 1. Once
every word has been read, divide the count for each word by the total number of words.
Words are case-insensitive. The simplest way to handle this is to convert words to upper- or
lowercase while reading.
Table 2 shows the WFD for a short example file. Note that “I” has been converted to lowercase
and that “can’t” and “cant” are treated as the same word (because the apostrophe is ignored).
Data structure You will need to maintain a list of mappings between words and counts (later
frequencies). You are free to choose any data structure, but you may find a linked list to be a good
balance of efficiency and simplicity. It is recommended that you choose a structure that allows you
to iterate through the words in lexicographic order.
Your program must not assume a maximum word length. Instead, word storage will be dynamically allocated.
3
(a) F1
hi 0.5
there 0.5
(b) F2
hi 0.5
out 0.25
there 0.25
(c) F
hi 0.5
out 0.125
there 0.375
KLD(F1||F) = 0.5 · log2

0.5
0.5

+ 0.5 · log2

0.5
0.375
≈ 0.5 · 0 + 0.5 · 0.415
≈ 0.2075
KLD(F2||F) = 0.5 · log2

0.5
0.5

+ 0.25 · log2

0.25
0.125
+ 0.25 · log2

0.25
0.375
≈ 0.5 · 0 + 0.25 · 1 + 0.25 · −0.585
≈ 0.1038
JSD(F1||F2) ≈
q
1
2
0.2075 + 1
2
0.1038
≈ 0.3945
Figure 1: Computing the JSD for two files
3.2 Jensen-Shannon distance (JSD)
The Jensen-Shannon distance (JSD) is a symmetric measure of the similarity of two discrete
distributions. We will write Fi(x) to mean the frequency of word x in file i. Note that Fi(x) = 0 if
x does not appear in file i.
We define the mean frequency for a word to be the average of its frequencies in the two files.
F(x) = 1
2
(F1(x) + F2(x)) (1)
Next we compute the Kullbeck-Leibler Divergence (KLD) between each file and the mean.
KLD(Fi
||F) = X
x
Fi(x) · log2

Fi(x)
F(x)

(2)
This is computed by adding the frequencies of each word in the file scaled by the base-2 logarithm
of the frequency divided by the mean frequency for that word. The result will be a value between 0
and 1.
Finally, the JSD is the square root of the mean KLD between the files and the mean distribution.
JSD(F1||F2) = q
1
2KLD(F1||F) + 1
2KLD(F2||F) (3)
Figure 1 shows the steps to compute the JSD for two files containing “hi there hi there” and “hi
hi out there”, respectively. Figures 1a and 1b give the WFD for the files, and fig. 1c shows their
mean WFD.
4
Directory
Queue
File
Queue
Directory
Threads
File
Threads
Main
Thread
Starts Starts
WFD
Repository
Figure 2: Organization of the collection phase
Implementation If you have chosen a WFD structure that allows you to iterate through the
word lists in alphabetical order, it is simple to compute the JSD using simultaneous iteration for
both lists. Keep a running total of the KLD for both files. If you encounter a word appearing in
both lists, compute the mean frequency and then add the scaled frequencies to both running totals.
If word appears in one list but not the other, treat its frequency as 0 in the file where it does not
appear. Once all words have been considered, compute the JSD.
4 Program organization
Your program will operate in two phases. The collection phase recursively traverses directories and
reads files to find the WFD (see section 3.1) for each requested file. The analysis phase computes
the JSD (see section 3.2) for each pair of requested files.
Both phases are multithreaded and use synchronized data structures to perform their tasks.
4.1 Collection phase
The collection phase uses two groups of threads to find the WFD for each file in a set of requested
files. It uses two synchronized queues to keep track of the directories and that need to be examined.
Figure 2 shows the organization of the collection phase. The components of the collection phase
are:
Directory queue Contains a list of directories that have been seen but not yet traversed. This
will be a synchronized queue (or stack) that must be unbounded.
File queue Contains a list of files that have been seen, but not yet examined. This will be a
synchronized queue (or stack) that may be bounded or unbounded.
WFD repository Once a file has been examined, its name, count of tokens, and WFD is added to
this structure. This may be any synchronized data structure. See section 3.1 for details of
how to represent the WFD.
5
Main thread The main thread creates the queues and repository. For each regular argument, it
determines whether it is a file or directory and adds it to the appropriate queue. Based on
the program parameters (see section 2.2), it starts the requested number of file and directory
threads. Once all the file threads have completed, it proceeds to the analysis phase.
Directory thread Each directory thread is a loop that repeatedly dequeues a directory name from
the directory queue and reads through its directory listing. Each directory entry is added to
the directory queue. Each non-directory entry that ends with the file name suffix is added to
the file queue.
A directory thread will finish when the queue is empty and all other directory threads have
finished or are waiting to dequeue.
File threads Each file thread is a loop that repeatedly dequeues a file name from the file queue,
tokenizes the file and computes its WFD, and adds the data for that file to the WFD repository.
A file thread will finish once the queue is empty and all directory threads have finished.
Note that the working directory is shared by all threads, so the directory threads will not be
able to use chdir(). Instead, they will need to concatenate the directory name and the file or
subdirectory name to get a path. Assume that all file and directory names given as arguments are
relative to the working directory (that is, you do not need to modify or examine them).
We will discuss synchronized queues in class, but you will need to customize them somewhat
to work here. When the directory queue is empty, you will need to keep track of the number of
threads waiting to dequeue. Once the last thread tries to dequeue, you can be certain that no new
directories will be found. At this point, you can set a flag indicating that traversal has ended and
wake up the directory threads so that they can terminate. Similarly, file threads should terminate if
the file queue is empty and traversal has ended (meaning no more files will be added).
Exercise Why is it safe for the file queue to be bounded, but not the directory queue?
Error conditions If any file or directory cannot be opened, report an error and continue processing.
It is sufficient to call perror() with the name of the file or directory to report the error. You may
also exit with status EXIT_FAILURE when the program completes.
For unexpected errors, such as failure to create threads or lock and unlock mutexes, your program
may report an error and terminate immediately.
4.2 Analysis phase
The analysis phase computes the JSD (see section 3.2) and combined word count for each pair of
files listed in the WFD repository (see section 4.1). It divides this work among one or more analysis
threads, as indicated by the analysis threads option (see section 2.2).
Each analysis thread is given a portion of the file pairs and computes the JSD for each pair. Once
all comparisons have been made, the main thread will sort the list of comparisons in descending
order of combined word count and then print the results.
6
Data structure For each comparison, we will need the names of the files being compared, the
combined word count, and the JSD. If there are n files, there will be 1
2
n(n + 1) comparisons, so it
is feasible to create an array of structs, have each thread write to non-overlapping portions of the
array, and finally sort the array using qsort().
Division of labor The simplest way to divide the work among the analysis threads is to give
each thread a roughly-equal portion of the comparison set to compute. If there are 30 files and 5
analysis threads, then each thread will compute 93 of the 465 comparisons. (Naturally, we must be
able ot handle cases where the number of comparisons does not divide evenly.)
While this method divides up the number of tasks (roughly) equally, it assumes that all
comparisons will take equally long to compute. Another method to divide the work is to keep
track of which comparison needs to be computed next and have each analysis thread take the next
comparison needed. This will reduce the possibility that some threads will finish early while other
threads have significant amounts of work left to do.
Error conditions If the collection phase found fewer than two files, report an error and exit.
Any numeric errors occurring in this phase (e.g., word frequencies outside the range [0,1]) indicate
problems in the collection phase. You may choose to check these using assert().
5 Advice
Don’t panic! While this assignment has many components, the components themselves are
relatively simple. If you begin before we have gone over synchronized queues in class, you can still
design your data structures and begin work on the analysis phase.
While use of the C file IO functions (e.g., fopen()) is permitted for this assignment, you will
not find them any easier or more convenient than using open() and read(). Using getline() will
just add complexity to your program for no real benefit.
Recall that printf() and fprintf() are synchronized, meaning they can be safely used in
different threads. During debugging, you may find it helpful to print log messages describing what
actions your threads are doing. Use the DEBUG macro trick to easily enable or disable these messages
as needed.
Always check for errors. Functions like malloc() or pthread_mutex_lock() never fail under
normal circumstances, which means you definitely want to be informed if they do fail—it may
indicate a logic error in your program! If writing the error checks becomes tedious, define a macro
to write them for you. How best to handle error conditions is a design choice, but the usual thing to
do when something “impossible” happens is to report an error and terminate the program.
That being said, checking printf() for an error result is probably overkill.
6 Submission
Submit a Tar archive containing your source code, makefile, and a README. The README must
contain:
7
• Your name and NetID1
• Your partner’s name and NetID, if you worked with a partner.
• A brief description of your testing strategy. How did you determine that your program is
correct? What sorts of files and scenarios did you check?
Do not include executables, object files, or testing data. Before submitting, be sure to confirm
that your archive contains the correct files!
For safety, both partners should create and submit an archive.
7 Grading
Your program will be scored out of 100 points: 50 points for each part. Your grade will be based on
test cases and on manual examination. Testing will be performed on iLab machines, so be certain
that your code will compile and execute on the iLab!
Your code should be free of memory errors and undefined behavior. We may compile your code
using AddressSanitizer, UBSan, Valgrind, or other analysis tools. You will lose points if these tools
report memory errors, space leaks, or undefined behavior. You are advised to take advantage of
AddressSanitizer and UBSan when compiling your program for testing.
Late submissions This project may be handed in up to 72 hours past the due date. Late
submissions will be penalized according to the following scale:
Up to Penalty
30 minutes 5%
2 hours 10%
24 hours 25%
72 hours 50%
Plan to complete your assignment early! The late submission grace period is provided for
emergency use and for last-minute salvage. Build slack into your schedule so that unexpected delays
or difficulties do not result in a late submission.
1
If you prefer not to share your NetID with your partner and/or Google, contact your TA and request a unique
identifier to use for this project.
8