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

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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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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About using graph-tool to find paths
by Minjian 03 Sep '15

03 Sep '15

I have noticed that graph-tool can be used to find shortest paths. I wonder can I use graph-tool to find paths with specific path length?? Many 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.

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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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Citation
by Flavien Lambert 23 Jul '15

23 Jul '15

Hi, could you tell me how to cite the project in a scientific paper? A bibTeX entry would be awesome! Best regards, F.

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close edges
by Bertrand Chapleau 17 Jul '15

17 Jul '15

Hello, I'm trying to find a way to spatially separate edges from each other in cases where two nodes are connected by many edges. This is done by default but I'd like them to be even more spread out so that I can put readable text on each edge. I've a feeling this can be accomplished by edge_control_points but can't figure out how to specify appropriate bézier control points. Any hints would be greatly appreciated ! Best, -bertrand

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Can't import graph-tool
by MichaelB 17 Jul '15

17 Jul '15

I try to import graph-tool in Python 2.7 with /from graph_tool.all import */ Each time I execute the above command the following error is returned and Python crashes. > dyld: lazy symbol binding failed: Symbol not found: > __ZN5boost6python6detail11init_moduleEPKcPFvvE > Referenced from: > /usr/local/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > Expected in: flat > namespace > dyld: Symbol not found: __ZN5boost6python6detail11init_moduleEPKcPFvvE > Referenced from: > /usr/local/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so > Expected in: flat namespace > Trace/BPT trap: 5 I installed graph-tool using homebrew on Mac OSX 10.10. Does anyone what's going on here? -- 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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About the usage of weights in shortest_path
by François Kawala 15 Jul '15

15 Jul '15

Hello, I don't get how the weight parameter is used in the shortest_path function when the pred_map is provided. More precisely the code: https://github.com/count0/graph-tool/blob/master/src/graph_tool/topology/__… seems to examine each and any edge when the weight parameter is provided. What is the point of this behavior ? what do I miss ? Best, f.

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