graph-tool May 2014

graph-tool@skewed.de

17 participants
24 discussions

Merging blocks in BlockState
by Joel Moberg 21 May '14

21 May '14

I want to implement a new community detection algorithm, like multilevel_minimize this is an agglomerative algorithm that will merge blocks. I now wonder whats a good way to merge whole blocks, I can move vertices between blocks with move_vertex to do this but is there a better way? Maybe a merge_blocks(blocks...) function could be useful.

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Creating an Erdos-Renyi Graph
by Helen Lampesis 19 May '14

19 May '14

Dear Friends, How one should create an Erdos-Renyi random graph with graph_tool? Equivalently, a “G_n_p" graph? I think, one could create a graph with -n- vertices and n*p edges and then use the random_rewire function with model=‘erdos’. Q1. Can I create the input graph of the random_rewire deterministically and rely on the random_rewire to actually do the shuffling? Q2. “Turning on” the edge_sweep option and the niter is it crucial for the graph’s randomness? And a small suggestion: given the popularity of this type of model, it might worth an example at the documentation, to “attract” more people. All the best, Helen PS. Small side-question: what is the fastest way to create a graph object with n vertices and m edges (any edges other than parallel and self-loops are allowed).

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pycairo problem in ./configure
by Nikos Kouvaris 16 May '14

16 May '14

Hi all, I successfully compiled grpah-tool in my Mavericks OSX using homebrew for the dependencies optional or not (i.e. expat, boost, cairo,...) the configuration was ./configure LDFLAGS="-L/usr/local/Cellar" PYTHON_EXTRA_LDFLAGS="-L/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Python" CPPFLAGS="-I/usr/local/include/sparsehash" PYTHON_VERSION="2.7.6" --with-numpy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy --with-scipy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy --enable-cgal-valgrind --disable-cairo make and make install works fine here !! ---------------------------------------------------------------- No we I am coming into the problems... I need to be able also to draw my graphs, and so I need to install it again with cairo I had installed cairo, cairomm, py2cairo (for python2.7) before with homebrew, as you can see $ pkg-config cairomm-1.0 --libs -L/usr/local/Cellar/cairomm/1.10.0/lib -L/usr/local/Cellar/cairo/1.12.16/lib -L/usr/local/Cellar/libsigc++/2.3.1/lib -lcairomm-1.0 -lcairo -lsigc-2.0 $ pkg-config pycairo --libs -L/usr/local/Cellar/cairo/1.12.16/lib -lcairo $ pkg-config cairo --libs -L/usr/local/Cellar/cairo/1.12.16/lib -lcairo Now I am trying to configure the installation as: ./configure LDFLAGS="-L/usr/local/Cellar" PYTHON_EXTRA_LDFLAGS="-L/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Python" CPPFLAGS="-I/usr/local/include/sparsehash" PYTHON_VERSION="2.7.6" CAIROMM_LIBS="-L/usr/local/Cellar/cairomm/1.10.0/lib -L/usr/local/Cellar/cairo/1.12.16/lib -L/usr/local/Cellar/libsigc++/2.3.1/lib" CAIROMM_CFLAGS="-O3 -lcairomm-1.0 -lcairo -lsigc-2.0" --with-numpy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy --with-scipy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy --enable-cgal-valgrind >> my_conf.log.txt and as you can see in the file my_conf.log.txt I take an error message: ....... checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... yes checking python module: cairo... yes checking pycairo/pycairo.h usability... no checking pycairo/pycairo.h presence... no checking for pycairo/pycairo.h... no configure: error: pycairo headers not found The whole files my_conf.log.txt as well as the config.log are attached here. Does anyone have the same problem or know how to solve it? Thanks in advance, Nikos

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random rewire
by david＠harsk.dk 16 May '14

16 May '14

Hi, I am trying to use the random_rewire function to generate a new network, using the 'correlated' model. The network is pretty small (208 vertices, 594 edges - no loops or parallel edges). If I just run it with default parameters, it rejects about 300-400 of the moves and 10000 iterations takes about 1 minute. To improve the shuffling a bit, I tried to add persist=True. Now the problem is, after 2 hours, it has not even completed a single iteration. I am suspecting that it is stuck in an infinite loop somewhere, but I cannot figure out why. Would there be any special property of a graph which causes this? For reference, these are the two commands I have tried executing: K = 10000 # Finishes in about 1 minutes for i in range(K): graph_tool.generation.random_rewire(testg, model='correlated') # After 2 hours and counting, still has not finished one iteration for i in range(K): graph_tool.generation.random_rewire(testg, model='correlated', persist=True) print "%i done" % i Also, the question I am trying to answer is, given the original graph and properties, what is the size of the largest connected component observed when the network is rewired at random, preserving node degree. Thanks in advance, David

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Graph database graph-tool
by blu-elephant 14 May '14

14 May '14

Interested to know if there are any plans to link graph-tool with a graph database e.g. via the Tinkerpop <http://www.tinkerpop.com/>stack of technology or pyBlueprints <https://github.com/escalant3/pyblueprints>? I would be great to be able to run the algorithms within graph-tool on data from a graph database (such as neo4j) without having to have a static GraphML representation of the data -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 2

Large Graph Visualization
by codejon 12 May '14

12 May '14

I haven't yet begun to use graph-tool, but it seems like a very good option for analysis of large graphs. I'll be using it to analyze graphs with 50-100,000 nodes, often densely connected (adjacency matrices are about 70% sparse). What I would like to know is how graph-tool will work for visualizing such graphs. I have tried a couple of stand-alone visualization programs with poor results. I would also like to have the option to embed the graph in three dimensions according to spatial coordinates that I specify. How will graph-tool suite my needs? If it's not optimal, can someone suggest a visualization tool that can be integrated with graph-tool without too much headache? Thanks in advance. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

2 4

Creating an isomorphic graph
by Helen Lampesis 10 May '14

10 May '14

Dear All, I would like, given an undirected graph G to create another instance of a graph object GP so that GP is isomorphic to G. Thus, the two graphs are essentially the same graph, and the only difference is they way internally are “numbering” the vertices. My intention is to look at their spectra. So far, I am doing this in a very expensive manner: take the adjacency of G, use its “dense” form, and then shuffle the rows/columns according to a random permutation. Can I do this more efficiently? I think it should be doable to traverse G (from a random node) and then build GP, as I am “exploring" G. The crucial thing is I want to avoid the “to dense()” operator on the adjacency matrix. Thanks a lot!

2 1

Build a graph from the adjacency matrix
by marklasta 10 May '14

10 May '14

Hi there ! I'm wondering if possible to build a graph starting from the adjacency matrix. Having such a matrix matrix = [[1.0, 0.0], [1.0, 1.0]] I'd like to build its graph (0) --- (0) (1) --- (0) (1) --- (1) Thank you in advance. Marco. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

2 1

Installation problem on Ubuntu 14.04 Trusty Tahr
by Legacy25 08 May '14

08 May '14

Hello, my name is Arindam Nandi, and I have been using the grpah-tool module for a college project. It was working absolutely fine on Ubuntu 13.04. Yesterday, I upgraded to the 14.04 LTS release of Ubuntu and tried installing the module the same way I did before, following the directions in your downloads page for Ubuntu. I added the lines deb http://downloads.skewed.de/apt/trusty trusty universe deb-src http://downloads.skewed.de/apt/trusty trusty universe to /etc/apt/sources.list, updated the repositories and then tried to install using sudo apt-get install python3-graph-tool But its giving me the following error: The following packages have unmet dependencies: python3-graph-tool : Depends: libpython3.3 (>= 3.3.3) but it is not installable E: Unable to correct problems, you have held broken packages. python-graph-tool is getting installed fine, but all my code is in Python3. I am a relative newbie to linux, so I am having trouble understanding what the problem is here, any help will be appreciated. Thanks. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

2 2

a function like "adjacent_vertices()"
by Miao 05 May '14

05 May '14

Hi, folks, My apology if it is a repeated questions! I briefly searched on the list for "adjacent vertices", but found most of the threads are about adjacency matrices. Basically, I am looking for a function similar to "adjacent_vertices()" defined in here: http://www.boost.org/doc/libs/1_55_0/libs/graph/doc/AdjacencyGraph.html It should simply return an iterator of all the adjacent vertices of a given one. I couldn't find such a straightforward function in graph-tool library. Do I have to use the Adjacent Matrix or some other fancy approaches? Thank you very much for providing this awesome python wrapper, since the python wrapper comes with BGL hasn't been updated for years. Cheers, Miao -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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graph-tool May 2014