June 2015 - graph-tool - archives.skewed.de

Help regarding -enable-openMP
by Shubham Bhushan 11 Nov '15

11 Nov '15

Hi I asked earlier as to how utilize the parallel processing in my code. Now I installed it using the precompiled packages for Ubuntu. does that mean I'll have to reinstall it from source using the openmp option in the configure command? Shubham -- http://about.me/shubham.bhushan

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Efficient Bipartite Projection
by Carlos Andrade 17 Sep '15

17 Sep '15

Dear all, I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that). I started of from (1) Gephi plugin ( https://marketplace.gephi.org/plugin/multimode-networks-transformations-2/) which after running for a couple hours almost froze my computer and output no graph (I had to force quit it). My second attempt was (and is) on igraph ( http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection ) I came across this post: http://stackoverflow.com/questions/606516/python-graph-library And read about graph-tool and how efficient it is compared to the igraph and networkx (which I was about to try but given up when I saw the time table). Thank you for your attention,

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graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> 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.

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Installation of graph-tool on Ubuntu 15.04
by cpblpublic+graphtool＠gmail.com 16 Jul '15

16 Jul '15

The instruction page https://graph-tool.skewed.de/download#debian suggests that packages are available for Ubunbu vivid (15.04), but it does not work for me. apt-get install python-graph-tool Reading package lists... Done Building dependency tree Reading state information... Done 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 resolve the situation: The following packages have unmet dependencies: python-graph-tool : Depends: libgv-python but it is not installable Depends: libboost-graph1.55.0 but it is not installable Depends: libcgal10 but it is not installable E: Unable to correct problems, you have held broken packages. There are no holds, according to "apt-mark showhold" I have tried numerous other things, but to no avail (from source, configure gets stuck on boost, even though it's installed). My configuration is fairly clean and simple. Have others had success on 15.04? Thank you!! Chris

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Load graph from csv
by kenanh 27 Jun '15

27 Jun '15

Hi, I'm loading directed weighted graph from csv file into graph-tool graph graph. The organization of the input csv file is: 1,2,300 2,4,432 3,89,1.24 ... Where the fist two entries of a line identify source and target of an edge and the third number is the weight of the edge. Currently I'm using: import csv g = gt.Graph() e_weight = g.new_edge_property("float") f_network = open(in_file_directory+ '/'+network_input, 'r') reader_network = csv.reader(f_network, delimiter=delimiter) for edge in reader_network: e = g.add_edge(int(edge[0]), int(edge[1])) e_weight[e] = float(edge[2]) f_network.close() However it takes quite long to load the data (I have network of 10 millions of nodes). I have tried to make it faster by using g.add_edge_list, but this works only for unweighted graphs. Any suggestion how to make it faster? -- 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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Python 2 compatibility
by Lukas Szabo 22 Jun '15

22 Jun '15

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How to increase canvas size?
by Ryan Compton 22 Jun '15

22 Jun '15

I'm having trouble with my vertex text running off the edge of the canvas. For an example see: http://ryancompton.net/assets/darknet-market-basket-analysis/evo_market_lab… I got the impression that "fit_view" with a float would scale things properly but it does not seem to change anything.

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Installing graph tool in cygwin
by Matthew McIntire 17 Jun '15

17 Jun '15

I am trying to install graph-tool on windows in the cygwin environment. I have managed to install all of the dependencies and successfully run the configuration script, but when I make, I get this: $ make make all-recursive make[1]: Entering directory '/home/mcintima/graph-tool-2.2.43' Making all in src make[2]: Entering directory '/home/mcintima/graph-tool-2.2.43/src' Making all in graph make[3]: Entering directory '/home/mcintima/graph-tool-2.2.43/src/graph' Making all in centrality make[4]: Entering directory '/home/mcintima/graph-tool-2.2.43/src/graph/centrality' CXX graph_betweenness.lo CXX graph_centrality_bind.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo CXX graph_trust_transitivity.lo CXXLD libgraph_tool_centrality.la /usr/lib/gcc/x86_64-pc-cygwin/4.9.2/../../../../x86_64-pc-cygwin/bin/ld: warning: --export-dynamic is not supported for PE+ targets, did you mean --export-all-symbols? .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2449): undefined reference to `graph_tool::GraphInterface::GetNumberOfVertices(bool)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2449): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::GraphInterface::GetNumberOfVertices(bool)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2659): undefined reference to `graph_tool::GraphInterface::GetNumberOfVertices(bool)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2659): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::GraphInterface::GetNumberOfVertices(bool)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2709): undefined reference to `graph_tool::ValueException::ValueException(std::string const&)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2709): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::ValueException::ValueException(std::string const&)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2726): undefined reference to `graph_tool::ValueException::~ValueException()' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x2726): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::ValueException::~ValueException()' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x275f): undefined reference to `graph_tool::ValueException::ValueException(std::string const&)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text+0x275f): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::ValueException::ValueException(std::string const&)' .libs/graph_betweenness.o:graph_betweenness.cc:(.text$_ZN10graph_tool14ActionNotFoundD1Ev[_ZN10graph_tool14ActionNotFoundD1Ev]+0x3c): undefined reference to `graph_tool::GraphException::~GraphException()' .libs/graph_betweenness.o:graph_betweenness.cc:(.text$_ZN10graph_tool14ActionNotFoundD1Ev[_ZN10graph_tool14ActionNotFoundD1Ev]+0x3c): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `graph_tool::GraphException::~GraphException()' ...and so on. I tried replacing --export-dynamic with --export-all-symbols in configure.ac, which just led to the same error. I also tried replacing all instances of --export-dynamic in the graph-tool folder, which just caused the compilation to crash sooner. Any help would be greatly appreciated. Thanks, Matthew McIntire

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Installation with anaconda python
by Arjun Chennu 16 Jun '15

16 Jun '15

Hi, this looks to be a very promising tool. I use the anaconda scientific python stack for most my work, and thought to compile graph-tool with that. The installer script detects this python version and attempts to compile with it. However, it runs into an error with checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... no checking for exit in -lboost_graph... (cached) no checking for exit in -lboost_graph-mt... no checking for exit in -lboost_graph-mt-py2.5... no configure: error: No usable boost::graph found The libboost-graph* libraries are installed systemwide. Attached is the config.log file for more information. I would appreicate some help in resolving this installation problem. Cheers, Arjun

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Probably copy-paste typo
by Артём Демьянов 07 Jun '15

07 Jun '15

Hello. Nothing special, but I found probably copy-paste misprint in documentation: https://graph-tool.skewed.de/static/doc/draw.html#graph_tool.draw.graph_draw *vprops* : dict (optional, default: None) Dictionary with the vertex properties. Individual properties may also be given via the vertex_<prop-name> parameters, where <prop-name> is the name of the property. *eprops* : dict (optional, default: None) Dictionary with the *vertex* properties. Individual properties may also be given via the edge_<prop-name> parameters, where <prop-name> is the name of the property.

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