digraph Example {
rankdir=LR;

node [shape="box",color="blue"]; q_0 q_1 q_2 q_3 q_4 q_6 q_7 q_8 q_9 q_10;
node [shape="circle",color="black"]; q_5;

q_0 -> q_1 [label="1"];
q_1 -> q_2 [label="1"];
q_2 -> q_3 [label="1"];
q_3 -> q_4 [label="1"];
q_4 -> q_5 [label="1"];
q_5 -> q_5 [label="0, 1"];

q_0 -> q_6 [label="0"];
q_1 -> q_7 [label="0"];
q_2 -> q_8 [label="0"];
q_3 -> q_9 [label="0"];
q_4 -> q_10 [label="0"];

q_6 -> q_7 [label="0, 1"];
q_7 -> q_8 [label="0, 1"];
q_8 -> q_9 [label="0, 1"];
q_9 -> q_10 [label="0, 1"];

q_10 -> q_0 [label="0, 1"];
}

A graph starts with “graph” or “digraph”, followed by its name. Properties of the graph are wrapped in a pair of accolades. In this example, the first property is “rankdir=LR“, which sets the orientation of the graph to left-to-right (instead of the default top-to-bottom). Line four and five define the appearance of each node used in the graph. At the end of this dot graph is a list of relations between the defined nodes. Below is the generated image of this graph.

automaton generated by GraphViz' dot graphs

On Debian(-based) distributions, you can install the required packages with the following command:

sudo apt-get install graphviz dot2tex gedit-latex-plugin

Configuring Gedit’s LaTeX plugin

Enable GeditLaTeXPlugin in Gedit using the menu Edit → Preferences. At the Preferences dialog, click on the tab “Plugins”, scroll down to “Gedit LaTeX Plugin” and check its checkbox. Close the dialog and restart Gedit.

GeditLaTeXPlugin does not natively support embedded dot graphs, because rubber is used to process the LaTeX documents instead of pdflatex. To fix this, you should open the following file:

sudo gedit /usr/lib/gedit-2/plugins/GeditLaTeXPlugin/tools.xml

At line number 3 and 7, you will find:

<job mustSucceed="true" postProcessor="RubberPostProcessor">
  rubber --inplace --maxerr -1 --short --force --warn all --pdf "$filename"
</job>

Replace the lines at line number 3 and 7 with the following:

<job mustSucceed="true" postProcessor="RubberPostProcessor">
  pdflatex -shell-escape -src -interaction=nonstopmode "$filename"
</job>

Fixing dot2tex

At the bottom of Gedit is a so-called “buttom-panel” containing tabs for a python console, terminal and LaTeX output (its tab name is “tools”). The latter one lists errors occurred during the compilation of a LaTeX document. The dot2tex script uses the deprecated module “md5″, which should be replaced by the module “hashlib”. Otherwise, a lot of useless warnings are logged in the LaTeX output tab. Edit the following file to fix these warnings:

sudo gedit /usr/share/pyshared/dot2tex/dot2tex.py

Scroll to line 2828 and replace the hashing code with the following lines of code:

import hashlib, cPickle
if len(args) == 1 and options.outputfile:
    log.info('Caching enabled')
    inputfilename = args[0]
    # calculate hash from command line options and dotdata
    md5 = hashlib.md5()
    md5.update(dotdata + "".join(sys.argv))
    inputhash = md5.digest()

Embedding dot graphs

Finally, it is time to demonstrate embedding dot graphs in a LaTeX document:

\documentclass[10pt,a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}

% dot graphs
\usepackage{dot2texi}
\usepackage{tikz}
\usetikzlibrary{shapes,arrows}

\author{Sander van Veen}
\title{Dot graphs in \LaTeX}

\begin{document}

\maketitle

\begin{dot2tex}[dot,options=-tmath --autosize --cache]
digraph G {
rankdir=LR;

node [shape="none"]; start ;

node [shape="box",color="blue"]; q_0;
node [shape="circle",color="black"]; q_1 q_2 q_3;

start -> q_0;

q_0 -> q_1 [label="1"];
q_1 -> q_0 [label="1"];

q_1 -> q_2 [label="0"];
q_2 -> q_1 [label="0"];

q_2 -> q_3 [label="1"];
q_3 -> q_2 [label="1"];

q_3 -> q_0 [label="0"];
q_0 -> q_3 [label="0"];
}
\end{dot2tex}

\end{document}

After “\begin{dot2tex}” are a couple of options shown used to alter the behaviour of dot2tex (-tmath substitutes for example _ with subscript, --autosize will reduce the dimension of the image and --cache will save the converted dot output). There are many possible options for dot2tex, which are documented in its manpage. Please note that dot2tex translates the dot format to tex (pstrikz to be exactly), and therefore does not support all features of dot.

Last but not least the output of the example LaTeX document: output PDF of embedded dot graph.

Packages installation

Using sudo or as root user:

sudo apt-get install git-core cmake g++ libboost-dev flex bison re2c libmysqlclient-dev libxml2-dev libmcrypt-dev libicu-dev openssl binutils-dev libcap-dev libgd2-xpm-dev zlib1g-dev libtbb-dev libonig-dev libpcre3-dev git-core autoconf libtool libcurl4-openssl-dev libboost-system-dev libboost-program-options-dev libboost-filesystem-dev

Getting HipHop source-code

mkdir hiphop
cd hiphop
git clone git://github.com/facebook/hiphop-php.git
cd hiphop-php
export CMAKE_PREFIX_PATH=`/bin/pwd`/../
export HPHP_HOME=`/bin/pwd`
export HPHP_LIB=`/bin/pwd`/bin
git submodule init
git submodule update
cd ..

Building third-party libraries

libevent

wget http://www.monkey.org/~provos/libevent-1.4.13-stable.tar.gz
tar -xzvf libevent-1.4.13-stable.tar.gz
cd libevent-1.4.13-stable
cp ../hiphop-php/src/third_party/libevent.fb-changes.diff .
patch < libevent.fb-changes.diff
./configure --prefix=$CMAKE_PREFIX_PATH
make
make install
cd ..

ICU4

wget http://download.icu-project.org/files/icu4c/4.2.1/icu4c-4_2_1-src.tgz
tar -xvzf icu4c-4_2_1-src.tgz
cd icu/source
./configure --prefix=$CMAKE_PREFIX_PATH
make
make install
cd ../../

libCurl

Make sure that your system time is correct, otherwise ./configure will fail.

wget http://curl.haxx.se/download/curl-7.20.0.tar.gz
tar -xvzf curl-7.20.0.tar.gz
cd curl-7.20.0
cp ../hiphop-php/src/third_party/libcurl.fb-changes.diff .
patch -p0 < libcurl.fb-changes.diff
./configure --prefix=$CMAKE_PREFIX_PATH
make
make install
cd ..

Building HipHop

cd hiphop-php
cmake .
make

Now, we have successfully compiled HipHop! The next post will contain information about using HipHop (compiling PHP code in various modes and circumventing some of HipHop’s limitations).

An example of a dot graph of XDebug's profiling log of DuoWorks' main page

Perhaps you already noticed that not every function is listed in the graph. This is because I generated the graph with the default threshold of at least 1% runtime. Every function with a runtime of less than 1% of 12 ms (= total runtime) is therefore not visible. These functions are useless to optimize anyway.

Installing XDebug

Installing XDebug is pretty easy, because it is available in the Ubuntu repositories.

sudo apt-get install php5-xdebug

After installing, we need to customize the XDebug configuration. Append the following lines to /etc/php5/conf.d/xdebug.ini:

[xdebug]
; enable profiler
xdebug.profiler_enable=On
xdebug.profiler_output_name=profiler-%s-%t
xdebug.profiler_output_dir=/tmp/xdebug

Note: please make sure that the profiler output directory exists. Otherwise XDebug wouldn’t be able to write its profiler logs.

Finally, we restart the web server (Lighttpd in this case).

sudo /etc/init.d/lighttpd restart

Profiling PHP scripts

After restarting the webserver, we can start profiling PHP scripts. Simply open your browser and go to a PHP page. The XDebug log will be saved in /tmp/xdebug/ on your webserver. Download the log file to your PC, save it as “xdebug.log” and we are ready to start inspecting the log.

Creating a dot graph from the XDebug log

Most of the times, images say more than a thousand words. Therefore we will generate a dot graph from the profiling log. We will use the xdebugtoolkit to convert the XDebug cachegrind (= “xdebug.log“) to a dot graph. Make sure that the cachegrind file is in the parent directory of the XDebugToolkit. The following line will install the XDebugToolkit:

svn co http://xdebugtoolkit.googlecode.com/svn/tags/0.1.3/xdebugtoolkit/ xdebugtoolkit

Make sure you have installed the GraphViz packages (which contains dot):

sudo apt-get install graphviz

Now, we can finally start generating the dot graph:

cd xdebugtoolkit/
cg2dot.py ../xdebug.log | dot -Tpng -o ../xdebug.png

As I mentioned in the introduction, the XDebugToolkit uses a default threshold of 1%. You can change this threshold by adding -t THRESHOLD to the argument list. If you want to disable the threshold, use -t 0 and all called functions and their runtime will be displayed. However, disabling the threshold is not recommended, because it will generate a huge graph. The following line will generate a graph with all called the functions:

cg2dot.py -t 0 ../xdebug.log | dot -Tpng -o ../xdebug-all.png

Enjoy profiling your PHP scripts!

Update: Added Daniel’s notes to the How-to. Thanks Daniel!

User Interface

• Galleries (with thumbnails)
• Grids
• Lists
• Treeviews
• Toolbars
  • Buttons
  • Dropdown boxes
• Tooltips

Website

• Breadcrumbs
• Typography
  • Code blocks
  • Headers
  • Lists (bullets and numeric)
  • Text
• Fieldsets
• Forms
  • Check- and radio boxes
  • Input boxes
  • Textareas

YouTube running in Prism

Prism allows you to browse web applications with an minimalistic user interface. Applications can be opened from the dock or a shortcut on the desktop. Just like normal applications!

This how-to installs prism from the binaries provided by Mozilla and not from the Ubuntu repository. The version in the Ubuntu repository is a bit out of date and therefore it misses some essential features.

First, we get the Prism binaries and move the folder to /usr/share/prism/.

mkdir prism
cd prism/
wget http://prism.mozilla.com/downloads/1.0b1/prism-1.0b1.en-US.linux-i686.tar.bz2
tar --bzip2 -xf prism-1.0b1.en-US.linux-i686.tar.bz2
sudo mv prism /usr/share/

Then its time to install the Flash Player. You need to install the Flash Player plug-in in each user directory, otherwise the Flash Player wouldn”t work for that user.

wget http://fpdownload.macromedia.com/get/flashplayer/current/install_flash_player_10_linux.tar.gz
tar xfz install_flash_player_10_linux.tar.gz

for path in /home/*
do
 if [ -d "$path" ]
 then
 mkdir -p $path/.prism/plugins
 cp install_flash_player_10_linux/libflashplayer.so $path/.prism/plugins/libflashplayer.so
 fi
done

After installing the Flash Player plugin, Prism is ready to use! You can now create shortcuts by running the following command:

/usr/share/prism

Enjoy the power of Prism!

sudo apt-get install apache2 subversion mysql-server python python-mysqldb

Download and install mod_python for Apache and enable the module.

sudo apt-get install libapache2-mod-python libapache2-mod-python-doc
a2enmod mod_python

You need to add the following to your “httpd.conf”, to add a simple setup of Trac:

<Location /projects/myproject>
 SetHandler mod_python
 PythonInterpreter main_interpreter
 PythonHandler trac.web.modpython_frontend
 PythonOption TracEnv /home/trac/myproject
 PythonOption TracUriRoot /projects/myproject
</Location>

Download and install Trac 0.10.4 from the ubuntu repositories.

sudo apt-get install trac

Download the ClearSilver source, extract the source and open the directory.

wget http://www.clearsilver.net/downloads/clearsilver-0.10.4.tar.gz
tar -xzf clearsilver-0.10.4.tar.gz
cd clearsilver-0.10.4/

To get ClearSilver working with python2.5, I had to change one line in “configure”. So open the file and add version “2.5″ to the allowed python versions.

vim configure

Go to line 6560, and change the line to:

python_versions="2.5 2.4 2.3 2.2 2.1 2.0 1.5 24 23 22 21 20 15"

and another line in “configure.in”:

vim configure.in

Go to line 250, and change the line to:

python_versions="2.5 2.4 2.3 2.2 2.1 2.0 1.5 24 23 22 21 20 15"

Build the new “neo_cgi.so” and copy it to the site-packages:

./configure
make
make install
cp python/build/lib.linux-x86_64-2.5/neo_cgi.so /usr/lib/python2.5/site-packages/neo_cgi.so

Create a new Trac-environment.

trac-admin /home/trac/myproject/ initenv

Test your installation by browsing to “http://localhost/projects/myproject“. An example page of Trac will be displayed. Happy bugtracking!