graph-tool January 2012

graph-tool@skewed.de

6 participants
7 discussions

Segmentation fault using shortest_distance
by Juan Manuel Tirado 20 Mar '16

20 Mar '16

Hi Tiago, I am trying to calculate the shortest distances of a graph after applying a filter. I have a code that looks like this: g=gt.load_graph("myGraph.xml",format="xml") #for later use distances = gt.shortest_distance(g) #extract the components of the graph comp = g.label_components(g) #This splits the graph in several components #I want to calculate the shortest distances #for the component 2 for example filtering = g.new_vertex_property("boolean") for v in g.vertices(): if comp[v]==2: filtering[v]=True else: filtering[v]=False #set the vertex filter g.set_vertex_filter(filtering) distances_comp=gt.shortest_distance(g) The last line of code rises a segmentation fault. I have plotted the graph with the filtered graph and its correct, also I can calculate the local_clustering_coefficient without problems. Am I doing something wrong? Is there any other way to filter the graph and calculate the shortest distances? Is this a bug? Thanks so much, Juan

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Parallel Processing
by Derek Ditch 21 Nov '13

21 Nov '13

I want to use graph-tool using the multiprocessing library in Python 2.6. I keep running into issues though with trying to share a full graph object. I can store the graph in a multiprocessing.Namespace, but it doesn't keep the dicts of properties. Example: def initNS( ns ): _g = Graph( directed = False) ns.graph = _g ns.edge_properties = { 'genres': _g.new_edge_property("vector<string>"), 'movieid': _g.new_edge_property("int"), } ns.vertex_properties = { 'personid': _g.new_vertex_property("int32_t") } """ Build property maps for edges and vertices to hold our data The graph vertices represent actors whereas movies represent edges """ # Edges _g.edge_properties["genres"] = ns.edge_properties['genres'] _g.edge_properties["movieid"] = ns.edge_properties['movieid'] # Vertices _g.vertex_properties["personid"] = ns.vertex_properties['personid'] ns.graph = _g ########## This initializes 'ns', which is a multiprocessing.Namespace. The problem is that for example, ns.edge_properties[ * ] tells me that the type isn't pickle-able. I tried to just skip that and use the _g.edge_properties to access it, but those dicts aren't carried over to the different process in the pool. Presumably b/c they aren't pickle-able. Any thoughts about how to fix this? (For those interested, I'm attempting to use the IMDbPy library to do some graph analysis on the relationships among actors and movies. Each process has it's own db connection and trying to populate the graph with actor and movie information in parallel since it's a pretty large and dense graph. Somewhere in the neighborhood of 250,000+ vertices for just a depth of three relationships) Thanks, -- Derek

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Apt installation fails on Debian Sid
by Tue V Jensen 27 Jan '12

27 Jan '12

Hi! I tried installing the graph_tool package as per the instructions on the download page, but apt-get fails with the following error: Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: graph-tool : Depends: libcgal7 but it is not installable It seems libcgal7 was recently renamed to libcgal8, as this is the only available package in both testing and Wheezy. Can I install using libcgal8, or will have to wait for a version compatible with this? Thanks! Tue -- 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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Installing in a virtual environment
by Hector 20 Jan '12

20 Jan '12

Hi all, I've tried to install graph-tool inside a virtual environment in multiple ways now, e.g. 1. pip install graph-tool 2. pip install http://downloads.skewed.de/graph-tool/graph-tool-2.2.15.tar.bz2 3. easy_install graph-tool 4. Running "configure-make-make install" from source The first three failed basically because there's no setup.py and the fourth one failed because it couldn't find numpy (which is already installed in the virtual environment). I could do a system-wide installation, but that's not what I want. Have you guys successfully installed graph-tool inside a virtual environment? Best, -- Hector

2 1

Veronoi Diagram and Data locality
by Dmitrijs Ledkovs 15 Jan '12

15 Jan '12

Hello, This is my first post =) To begin with - what an awesome package! The website is great, the docs are amazing, the code is beautiful, sane autotools usage, very fast, pythonic! Best software package ever! I'm a beginner in graph theory. Any suggestions on books/tutorials which can quickly take me from basics to advanced topics would be appreciated. Now the question. I'm doing numerical simulation over a veronoi graph. I'm storing data on the vertexes and edges. The iterations go as following: 1) Using data on the edges ('incident pulses') I'm calculating the value of the vertex ('node voltage') 2) Using value of the vertex, I'm calculating new values for the edges ('scattered pulses') 3) During next timestep scattered pulses become incident - repeat In the future I may need to use symmetric directed graph and do more fun things with incident and scattered pulses. Now the slight problem arrises, when my graph + values is bigger than I can store in RAM. There is Global Arrays toolkit, which recently got GAiN (Global Arrays in Numpy) which allow seamlessly use numpy/scipy over shared memory cluster. But it will give good performance if arrays are exercising data locality properties. In my case I want property maps of vertixes & edges to be 'near each other' based on connectivity. Such that my algorithm computes as many vertexes/edges locally as possible. E.g. for a 2D latice I'm using http://en.wikipedia.org/wiki/Z-order_curve. Now I want something similar but for veronoi diagram. I'm not familiar with graph theory, but I was playing around with graph-tool and it seems like betweenness and/or communities give me something what I want. Ideally I want to retrieve indexes which will sort PropertyMap to exhibit data locality properties (Similar to Z-order curve). Does graph-tool already does something like this? Regards, Dmitrijs.

2 1

Building on windows (windows 7 64 bit building for win32)
by Noon Silk 09 Jan '12

09 Jan '12

Hello, Has anyone had much luck with this? I've been trying under cygwin with very little luck. Specifically I'm running ./configure, and it runs for a reasonable period of time (after I installed various requirements), but am now getting: checking for boostlib >= 1.38.0... yes checking whether the Boost::Python library is available... no configure: error: No usable boost::python found Even though I feel like claiming that there is indeed a viable boost::python available (that is to say, I claim I've installed it). Is there any hope for me here? Is there a better way to get it running (as a part of a .exe) under windows? I'll continue onward, but would love some words of encouragement, if anyone has them ... -- Noon Silk Fancy a quantum lunch? http://groups.google.com/group/quantum-lunch?hl=en "Every morning when I wake up, I experience an exquisite joy — the joy of being this signature."

2 1

graph-tool on Mac OS Lion - running!
by Sebastian Weber 02 Jan '12

02 Jan '12

Hi! Wonders seem to happen once in a while. Finally I got graph-tool running on my Lion machine. Here are my steps which lead to a running graph-tool: 1. deinstall Macports python 2.7 such that it is never in the way (reinstall whatever you need in macports with python with the python26 branch) 2. install boost 1.47.0 into $HOME/.local; linked against python 2.7 from apple 3. install numpy/scipy from the SuperPack, see scipy.org 4. install cgal 3.9 with gmp and other dependencies coming from macports; install dir is $HOME/.local 5. grab graph-tool from git and configure it with PYTHON_VERSION=2.7 PYTHON=/usr/bin/python2.7 CXXFLAGS="-I/$HOME/.local/include -I/opt/local/include" CFLAGS="-I$HOME/.local/include -I/opt/local/include" LDFLAGS="-L$HOME/.local/lib -L/opt/local/lib" ./configure --prefix=$HOME/.local --with-boost=$HOME/.local/ --with-numpy=/Library/Python/2.7/site-packages/numpy-2.0.0.dev_3b3735d_20111219-py2.7-macosx-10.7-x86_64.egg/numpy/ --with-scipy=/Library/Python/2.7/site-packages/scipy-0.11.0.dev_c2ff01c_20111219-py2.7-macosx-10.7-x86_64.egg/scipy/ --disable-debug --disable-openmp Compile it a very long time and then install it. Of course, I use the latest Xcode 4.2.1. I found it really hard to get graph tool running on Lion. Cheers, Sebastian -- Sebastian Weber Group of Cell Communication and Control Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universität Freiburg Albertstr. 19 79104 Freiburg T.: +49-761-203-97237 Fax:+49-761-203-97334

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graph-tool January 2012