Saint's Log


Modelling the Infamous Dining Philosophers

A sample implementation of the dining philosophers problem is provided in the JPF core source code. The solution I gave to this problem was to use the following locking scheme: if a thread has an even id i, then it should lock fork i first and then fork (i + 1) % N. If its id i is odd, then it should lock fork (i + 1) % N first and then lock fork i. Replacing

new Philosopher(forks[i], forks[(i + 1) % N]);


Fork leftFork, rightFork;
if (i % 2 == 0) {
    leftFork = forks[i];
    rightFork = forks[(i + 1) % N];
} else {
    leftFork = forks[(i + 1) % N];
    rightFork = forks[i];
new Philosopher(leftFork, rightFork);

Should do the trick. DiningPhil.jpf can then be launched to verify the absence of deadlock with this new locking scheme.


Getting into Motorcycling

I've had the desire to learn how to ride a motorcycle for a few years now. This summer, I decided to act on this bucket list item and enrolled in the Basic Rider Course with UtahRiderEd. I signed up for the weekend option. The classes ran all day Saturday and Sunday (until about 5pm). We were given a Motorcycle Safety Foundation text (from which the written portion of the test administered on Sunday came). My classes were at Murray High School and my bike for the course was a blue Yamaha XT225. Below are a few pictures of the setup. I now have my 649cc and below endorsement on my DL. It was nice only having to take the written test at the DLD since the MSF course eliminates the need for a road test. Now, to get a bike... a Ninja perhaps, anyone?


Copying Image Files to Build Folder in Eclipse

Part of my Google Summer of Code project this summer involved building a visualization tool to help examine trace files used by JPF Guided Test and a related under-approximation scheduler. The visualization tool is in the Guided Test repository. I was using Eclipse to manage the project. Everything built correctly but the program didn't work because the icons were not in the build folder as expected. A quick hint from stackoverflow was that the solution is to use Ant.

<target name="-pre-jar" description="Copy Images">
  <property name="images.dir" value="build/main/edu/byu/cs/guided/search/visualize/graphics" />

  <copy todir="${images.dir}">
    <fileset dir="./src/main/edu/byu/cs/guided/search/visualize/graphics" />
  <echo level="info" message="Visualization icons was copied."/>

The key is to use the "-pre-jar" target in the build.xml file to copy the files into the right spot. This change was part of the visualization check-in into the repository. Some documentation on Ant targets is available in the Apache Ant User Manual. This StackOverflow entry on adding resource files to a jar file with Ant has some useful hints as well.

Filed under: JPF No Comments

Attaching Java Source Files to an Eclipse JRE

As per this ubuntu thread, the solution is:

  1. Window > Preferences > Java > Installed JREs.
  2. Double click on the JRE for which you want to attach source code.
  3. Under "JRE System Libraries", select rt.jar.
  4. Click on the "Source Attachment..." button.
  5. Supply a path to the source zip file, e.g. C:/Program Files/Java/jdk1.6.0_23/

That zip file was already on my system (since the JDK was installed) but some projects were using the JRE rather than the JDK. Therefore, I needed to specify the JDK source zip file for the JREs as well.

Filed under: Eclipse No Comments

Creating a Rudimentary Tokenizer for the Delicious Data Set

In order to tokenize all the files in the Delicious data set to facilitate searching, I came up with the following basic scheme:

  1. Decode all XML entities leaving only the actual character they represent (see html_entity_decode).
  2. Strip out all HTML tags (see strip_tags).
  3. Convert everything to lower case (see strtolower).
  4. Strip out all numbers using the \b\d+\b regular expression (see preg_replace).
  5. Remove all non-alphabetic characters left.
  6. Collapse multiple spaces into one space.

This strategy translates very cleanly into PHP as shown below:

class WordTokenizer
	public static function tokenizeFile($file)
		$contents = file_get_contents($file);
		$contents = html_entity_decode($contents);
		$contents = strtolower(strip_tags($contents));
		// strip numbers
		$contents = preg_replace('/\b\d+\b/', ' ', $contents);
		// strip punctuation symbols & non-alphabetic symbols
		$contents = preg_replace('/[^a-z]/', ' ', $contents);
		// replace multiple spaces with just one
		$contents = preg_replace('/\s+/', ' ', $contents);
		return $contents;

The full source code is available in the information retrieval repository.


Setting Up a Tag Database for the Delicious Data Set

One of my assignments this past semester involved performing search operations on the tags supplied with the delicious data set. I created a database named "contentindex" and then a table for the tag information from the XML file using the following SQL:

	`docname` VARCHAR(255) NOT NULL,
	`tagname` VARCHAR(255) NOT NULL,
	`weight` INT NOT NULL,
	UNIQUE index_doc_tag_pair_weight (`docname`, `tagname`)

I set up an Eclipse Java project for the assignment. The MySQL Connector/J JDBC driver is required for interaction with the database. You will need to add it to the unzipped JAR file to the Delicious Eclipse project. To do so, right click on the project -> Build Path -> Add External Archives...

A list of XML parsers that could be used on the tag info XML file is available on the SAX website. I settled on the Xerces parser. Setup was a straightforward extraction into a folder, creation of a corresponding Java project in Eclipse, and finally adding the Xerces project to the Delicious Eclipse project's build path - Right click on the project -> Build Path -> Configure Build Path.... -> "Projects" Tab -> Add...

The source code for the XML tag info parser is available on my github repo.


Setting up an Amazon AMI

Start with the CS462 AMI.

Edit multiverse.list

sudo vi /etc/apt/sources.list.d/multiverse.list

Add the following lines to multiverse.list:

deb karmic multiverse
deb-src karmic main

Then run the following commands:

sudo apt-get update
sudo apt-get install apache2
sudo apt-get install php5 php5-cli php-pear php5-gd php5-curl
sudo apt-get install libapache2-mod-php5
sudo apt-get install libapache2-mod-python
sudo apt-get install ec2-ami-tools
sudo apt-get install ec2-api-tools
sudo apt-get install python-cheetah
sudo apt-get install python-dev
sudo apt-get install python-setuptools
sudo apt-get install python-simplejson
sudo apt-get install python-pycurl
sudo apt-get install python-imaging
sudo apt-get install subversion
sudo apt-get install git-core

Note: the sun-java6-bin and libphp-cloudfusion packages are not strictly necessary (OpenJDK will be installed instead of the former, and the AWS PHP SDK instructions are given below instead of the latter). unzip could come in handy as well. The python packages are installed to allow for python web development without having to install the appropriate packages after starting the server.

git config --global "Johny Boy"
git config --global
sudo vi /etc/apache2/sites-available/default

Next, install Smarty as per the Smarty documentation (lines 1-3) and the Zend Framework as well (lines 4-7) since it may come in handy.

cd /usr/local/lib
sudo wget
sudo tar vxzf Smarty-3.0.7.tar.gz
cd /opt
sudo wget
sudo tar vxzf ZendFramework-1.11.4-minimal.tar.gz
sudo mv ZendFramework-1.11.4-minimal ZendFramework-1.11.4

Install System_Daemon as well to enable running PHP Daemons. There's also a sample daemon illustrating how to use this class.

sudo pear install -f System_Daemon

Clone the AWS PHP SDK into /usr/share/php as documented in the "Getting Started with the AWS SDK for PHP" tutorial (lines 1-3) and then configure the SDK security credentials (lines 4-6).

sudo mkdir -p /usr/share/php
cd /usr/share/php
sudo git clone git:// awsphpsdk
mkdir -p ~/.aws/sdk
cp /usr/share/php/awsphpsdk/ ~/.aws/sdk/
vi ~/.aws/sdk/

Now we can prepare to create the image and then run the ec2 commands to create, upload, and register the image. See the AMI tools reference for information about these commands. Of course the actual access key, secret key, bucket names, etc need to be substituted with the correct values.

cd /mnt
sudo mkdir image
sudo mv /home/ubuntu/PrivateKey.pem .
sudo mv /home/ubuntu/X509Cert.pem .
sudo ec2-bundle-vol -k PrivateKey.pem -c X509Cert.pem -u 999988887777 -d /mnt/image
sudo ec2-upload-bundle -b cs462-machines/mybucket -m /mnt/image/image.manifest.xml -a AKIADQKE4SARGYLE -s eW91dHViZS5jb20vd2F0Y2g/dj1SU3NKMTlzeTNKSQ==
ec2-register cs462-machines/mybucket/image.manifest.xml --K PrivateKey.pem -C X509Cert.pem

Once the process is complete, the instance can be launched with the following user data:

#! /bin/bash
sudo git clone git:// /home/ubuntu/www > /home/ubuntu/gitclone.log
sudo chown -R ubuntu /home/ubuntu/www/
sudo chown nobody:nogroup /home/ubuntu/www/smarty/templates_c/
sudo chown nobody:nogroup /home/ubuntu/www/smarty/cache/
sudo chmod 770 /home/ubuntu/www/smarty/templates_c/
sudo chmod 770 /home/ubuntu/www/smarty/cache/

Note that the owner of the checked out www folder is set to ubuntu to ensure files can be edited conveniently without sudo. The "nobody" user is then made the owner of the smarty folders and they are assigned to the "nogroup" group. The permissions are then set to 770 for maximum security. I actually ended up using 777 to speed up development on my server - see the apache error log if nothing is displayed from the templates (most likely a case of permission errors).

Here's are some options to include in the apache configuration file:

        DocumentRoot /home/ubuntu/www/htdocs
        <Directory /home/ubuntu/www/htdocs/>
                Options Indexes FollowSymLinks MultiViews
                AllowOverride None
                Order allow,deny
                allow from all

                DirectoryIndex index.php index.html

                AddHandler mod_python .py
                AddHandler php5-script .php
                PythonHandler mod_python.publisher
                PythonDebug On

I ended up pushing my server configuration as well to a public git server containing my entire application. Server configuration is then reduced to:

sudo cp /home/ubuntu/www/serverconfig/apache/appserver/default /etc/apache2/sites-available/default
sudo apache2ctl restart

Building Racket in Linux

The Racket website has documentation on how to clone the PLT repository.

git clone git://

Next, the src/README file has all the gory details on how to build Racket. The procedure is rather straightforward for Linux:

mkdir build
cd build
make install

I'm yet to figure out how to successfully build racket in Visual C++ (2008 Professional), so that's the next item on my list.

Update (03/11/11): Actually rather straightforward for Visual C++ as well, run vsvars32.bat to ensure that devenv and other commands are in the path:

cd plt\src\worksp\
"C:\Program Files (x86)\Microsoft Visual Studio 9.0\Common7\Tools\vsvars32.bat"

I got the hint from this thread.


Implementing canvas putImageData’s optional arguments

BugĀ 498826 is about the HTML canvas putImageData method. It did not implement the optional arguments specified in the WHATWG spec. These optional arguments specify the dirty rectangle for the image data transfer (specifically, these arguments are the coordinates of the top left corner and the dimensions of the dirty rectangle, any of which are allowed to be negative). A quick glance at the description of the algorithm for handling of the optional arguments may not reveal the overall intent of the algorithm. Some of its key aspects are:

  1. Adjusting the dimensions of the rectangle to be positive by shifting the top left corner if necessary (step 2).
  2. Ensuring the top left corner of the dirty rectangle is in the first quadrant (step 3) which effectively eliminates all negative arguments.
  3. Clipping the dirty rectangle to ensure its lower right corner does not extend beyond the bounds of the incoming imagedata's dimensions (step 4).
  4. Verifying that the newly adjusted dirty rectangle has positive dimensions (step 5), and if so, using the region bounded by the dirty rectangle on the incoming imagedata object as the source for the operation.

The patch is rather straightforward (although admittedly, it was not as straightforward to create on my part). If there are enough arguments to specify a dirty rectangle, then the JS_ValueToECMAInt32 function is used to convert the JavaScript values into integers. The CheckedInt32 and the gfxRect classes do most of the heavy lifting in the patch, and then only the dirty rectangle is redrawn.


Remove unused nsCookieService::SetCookieString argument

Bug 520914 is the only Bugzilla item I got to look at this month - since it required the least amount of time :). All that needed to be done was to remove the aPrompt argument currently in nsICookieService's SetCookieString method. The locations in need of change were easily located with a simple MXR search.