# graph-toolEfficient network analysis

Graph-tool is released under the GPLv3. For general installation instructions, please see the included INSTALL file.

## Compilation

Graph-tool was tested extensively only on GNU/Linux and MacOS X systems, but should also be usable on other systems where the below requirements are met.

• GCC, version 4.8 or above (version 4.9 is recommended). For MacOS X, the clang compiler is required.
• The Boost libraries, version 1.54 or above.
• Python version 2.7 or 3 and above.
• The expat library.
• The SciPy python module.
• The Numpy python module.
• The CGAL C++ geometry library, version 3.5 or above.
• The sparsehash template library (optional, but recommended).
• The GTK+ 3, cairomm, pycairo and matplotlib libraries, used for graph drawing (optional).
• The Graphviz packaged for graph drawing, with the python bindings enabled (optional, deprecated).

Having installed the above dependencies, the module can be compiled in the usual way:

$./configure$ make

After compilation, the module can be installed in the default Python module directory by running:

\$ make install

#### Note for MacOS X users

Although graph-tool is a Python library, it is implemented in C++, and thus has C++ dependencies such as Boost, CGAL and expat, which are not installable via Python-only package management systems such as pip or EasyInstall. Unlike most GNU/Linux distributions, the MacOS X system does not include integrated package management with automated dependency tracking, which means that the dependencies would have to be installed individually by hand. Since they also have their own dependencies, this would trigger the manual installation of many libraries, which is quite time consuming, and is not recommended. Instead, the best option is use one of the third-party package management software available, such as Macports or Homebrew. The recommended choice is Macports, which allows the installation of graph-tool with a single command:

port install py-graph-tool

See below for more notes on installing on MacOS X, as well as the FAQ.

#### Memory requirements for compilation

Graph-tool requires large amounts of RAM (~4 GB) during compilation, because it uses lots of template metaprogramming. The supported compiler, GCC, is still not very well optimized for this, which means that even though the program is relatively small, it will still use up lots of RAM during compilation, specially if optimizations are used (and you do want to use them). See for instance GCC bug 12850.

An alternative is to use the clang compiler, which requires about half as much RAM, but tends to generate sightly slower code, and currently lacks OpenMP support.

#### Parallel algorithms

graph-tool can run several of its algorithms in parallel. It makes use of OpenMP to do this, which provides a straightforwards way of converting serial code into parallel code. OpenMP is an extension to the Fortran, C and C++ languages, which uses compiler directives to achieve automatized code parallelization. Since it uses compiler directives (#pragma in C/C++), it maintains backwards compatibility with compilers which do not support OpenMP, and the code is then compiled cleanly as regular serial code. Thus, support for parallel code in graph-tool is quite optional. If you wish to enable it, just pass the option "--enable-openmp" to the configure script.

## Pre-compiled Packages

### Debian & Ubuntu

where DISTRIBUTION can be any one of

jessie, sid

For Ubuntu, add the following lines

where DISTRIBUTION can be any one of

trusty, utopic

After running apt-get update, the package can be installed with

apt-get install python-graph-tool

or if you want to use Python 3

apt-get install python3-graph-tool

If you want to verify the packages, you should use the following public key: 98507F25.
After saving it to a file, you should add it to your list with

Afterwards, you can run apt-key list, which should give you the following details about the key:

pub   4096R/98507F25 2013-10-17 [expires: 2018-10-16]
uid                  Tiago de Paula Peixoto <tiago@skewed.de>
uid                  Tiago de Paula Peixoto <tiago@itp.uni-bremen.de>
sub   4096R/1A7ECE03 2013-10-17 [expires: 2018-10-16]
sub   4096R/23F08CAF 2013-10-17 [expires: 2018-10-16]

### Gentoo

An ebuild for graph-tool is included in the default Gentoo repository. Just do

emerge graph-tool

to install it.

### Arch

Packages for Arch are available in the Arch User Repository. You can install it with yaourt:

yaourt -S python2-graph-tool

or

yaourt -S python-graph-tool

depending on the python version. Thanks to Daniel Müllner for providing the installation scripts!

### MacOS X

#### Macports

A portfile is available for installation in MacOS X systems with Macports. It is included in the standard macports list. Just run the following command to install it:

port install py-graph-tool

If you want to install the latest development version from git, you can use this portfile.

#### Homebrew

Instructions for installation with Homebrew are available here. (Courtesy of Massimo Menichinelli)

#### Compiler choice in MacOS X

TL;DR : Just use clang for everything.

Make sure you use the same compiler to compile the whole stack (Python, Boost, etc) or you may lead into problems. Since more recent versions of graph-tool, a compiler which supports C++11 is required.

In an ideal world, the correct version should be the latest one from the "stock" FSF GCC, however it does not seem to be very well supported in the platform, and will lead to strange segfaults when using the library. The bastardized version from Apple (currently version 4.2) seems to work properly on the platform, but is too outdated to compile graph-tool (i.e. it fails to compile valid C++ code, and does not support C++11 properly), and is being deprecated. The clang compiler seems to be the only viable option on the platform, and should therefore be used.

(If possible, a much better option would be to use a less defective platform in the first place.)

#### FAQ for installation in MacOS X

Q: Why can't this be installed via pip? Why so complicated?
A: See note for MacOS X users above. The short answer is that it can't be done, since graph-tool depends crucially on some (excellent) C++ libraries such as Boost, which are not installable via pip.
Q: When importing the module, I get the following errors:
ERROR:root:Could not find any typelib for Gtk
ERROR:root:Could not find any typelib for Gdk
ERROR:root:Could not find any typelib for GdkPixbuf
A: Make sure you have XQuartz installed, as well as GTK+ 3 (gtk3 port in Macports).
Q: When attempting to draw a graph to the screen, I get the error:
gi._glib.GError: Couldn't recognize the image file format for file '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/draw/graph-tool-logo.svg'
Exception AttributeError: "'GraphWindow' object has no attribute 'graph'" in > ignored
A: You probably don't have the standard librsvg library installed. This can be installed with macports as follows:
port install librsvg
Q: I get unresolved symbol errors when importing the module, something like:
>>> import graph_tool
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
Expected in: flat namespace
A: This is due to different flavors of the C++ standard library (libc++ and libstdc++) being used for Boost and graph-tool itself. This is resolved by either compiling everything using clang with c++11 mode activated (which could be cumbersome, since the same would have to be done for everything else which uses Boost), or simply by upgrading to Mavericks (see here for more info).

## Git Repository

We use Git for source revision control and code sharing. The whole tree can be checked out with the following command:

git clone git@git.skewed.de:count0/graph-tool.git

For further instructions on how to use Git, see the documentation.

The git public repository can be browsed online here.

The git repository is also mirrored at github and gitorious