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lfrwmx

Matlab wrapper for weighted Lancichinetti-Fortunato-Radicchi benchmark graphs

Lancichinetti-Fortunato-Radicchi benchmark functions

Lancichinetti-Fortunato-Radicchi benchmark is a network generator for benchmark of community detection algorithms.

In this release I've adapted and partially rewritten the freely-available code (https://sites.google.com/site/santofortunato/inthepress2) to generate weighted networks as described in the paper by Lancichinetti A. and Fortunato S., Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities, Phys. Rev. E 80, 016118.

Requirements

  • Linux with GCC/G++ compiler (or other suitable C++ compiler)
  • CMake (www.cmake.org)
  • git

To compile clone this dataset:

$> git clone --recursive https:/github.com/CarloNicolini/lfrwmx.git
$> cd lfrwmx
$> mkdir build
$> cd build
$> cmake ..

The --recursive option is necessary as LFRWMX depends on Eigen libraries, and they are included as a submodule here. For the compilation of the MEX file you need MATLAB mex headers, usually installed with a standard Matlab installation.

You can compile the LFR benchmark by specifying:

$> cmake -DMATLAB_SUPPORT=True ..
$> make lfrw_mx

The wrapper is also available for Octave, in case you don't have MATLAB, just install the octave-mex headers (typically on Debian based distros: sudo apt-get install octave liboctave-dev)

$> cmake -DOCTAVE_SUPPORT=True ..
$> make lfrw_mx

FAQ

Linking libstdc++.so.6 problem

I can compile Paco for MATLAB but after calling paco_mx, MATLAB prompts me with the following error message:

Invalid MEX-file '~/paco_mx.mexa64': /usr/local/MATLAB/R2015a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ...

This problem means that the libstdc++.so.6 inside the Matlab library folder is pointing to a version of libstdc++ older than the system one, usually stored in /usr/lib/x86_64 folder.

To solve the issue you need to redirect the symbolic links in the MATLAB folder to the systemwise libstdc++. Hereafter we assume the MATLAB folder to be /usr/local/MATLAB/R2015a and the system to be some Linux variant.

Two of the symlinks for libraries need to be changed:

$> cd /usr/local/MATLAB/R2015a/sys/os/glnxa64
$> ls -l

The sym links for libstdc++.so.6 and libgfortran.so.3 should point to versions in /usr/lib, not local ones.

Before changing this libraries, first make sure g++-4.4 and libgfortran3are installed :

$> sudo apt-get install g++-4.4 libgfortran3

Now, modify the symlinks:

$> sudo ln -fs /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 libgfortran.so.3
$> sudo ln -fs /usr/lib/gcc/x86_64-linux-gnu/4.4/libstdc++.so libstdc++.so.6

This command makes the libstdc++.so.6 point to the g++-4.4 libstdc++ library.

The lfrw_mx function is self-documented:

LFRW: Lancichinetti-Fortunato-Radicchi network generator
This program produces weighted adjacency matrices for graph community detection benchmark
[WeightedGraph, membership] = lfrw('argname',argvalue);
Input:
'N'
    Desired number of nodes in the network
'k'
    Desired average degree of the network
'maxk'
    Desired max degree of the network
'minc'
    Desired minimum size of the community
'maxc'
    Desired maximum size of the community
'mut'
    Desired community topological mixing coefficient (range [0,1])
'muw'
    Desired weights mixing coefficient (range [0,1])
't1'
    Desired exponent for the degree distribution
't2'
    Desired exponent for the community size distribution
'beta'
    Desired beta exponent
'C'
    Desired clustering coefficient
Error using lfrw_mx
Error at argument: 0: Not enough input arguments.