August 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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Importing legend in Graph-tool
by amir moahmad hatami 03 Sep '15

03 Sep '15

I am trying to plot a graph of websites but the names are long. and the plot is not good i want to number each site and then beside the picture name which number is for which site. could help me how to do it? 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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specifying the number of cores
by ostrokach 26 Aug '15

26 Aug '15

Hi, I was wondering if there is a way to specify the number of cores that graph-tool uses for OpenMP algorithms? I couldn't find it looking through documentation and the mailing list. It would be nice if you could set n_cores=1 when running graph-tool on a cluster, for example, and set n_cores=4 when running on a local machine. Thanks, and sorry if this has been asked before, Alexey -- 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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Most efficient way to model an epidemic?
by gogurt 23 Aug '15

23 Aug '15

Hi all, So I've scoured the documentation for this but I've been indoctrinated in the ways of NetworkX, so I'm pretty confused. I want to implement a simple discrete-time epidemic process on a network. For example, starting out with one infected vertex, I want to explore all its out-neighbors and infect those with probability p, and then the neighbors of those out-neighbors, etc. Once you're infected, you are infected forever. The way I've done this in NetworkX is to essentially keep track of 3 lists of nodes (infected, active, unexplored) and update them in a simple loop. Then at the end of the process when the epidemic dies or hits a threshold, I just subset the graph and get the subgraph which represents the path of the infection. *My question is: *what's the most efficient way to do this using graph-tool? At first I thought the same approach (subsetting vertices, which would mean working with vertex iterables) would be the fastest way, but then I thought maybe working on the original graph with a vertex PropertyMap would be better. But my intuition is extremely poor on this (e.g. is it even possible to subset vertices in a graph based on their values in a PropertyMap object?). Any pointers? -- 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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graphviz_draw crashing?
by gogurt 20 Aug '15

20 Aug '15

Hi all, Lately I've been drawing graphs using the sfdp layout on graphviz_draw. About 2 weeks ago before I installed some Python updates (not sure which exactly), I had no problem drawing trees using this method. When I run it I get the Spyder error "It seems the kernel died unexpectedly. Use 'Restart kernel' to continue using this console." so something seems to be crashing. I'm using Python 3.4.3. with graph-tool version 2.2.44. Any ideas what might be happening? -- 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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Geometric graph generation: possible bug, difficult to re-produce
by mh 18 Aug '15

18 Aug '15

Hello, I apologise I can't give a better bug report than this, but I've been playing with generating geometric graphs using graph-tool. I think the periodic boundary conditions may not be working properly in some cases, literally I think corner cases, or maybe there's a rounding error of some kind? I was trying to create a hexagonal close packed-like geometric graph. (I'm fairly new to graph analysis, and I've been struggling to come up with a good example that would show this bug because I'm finding it difficult to track down exactly which edges are missing, but I'm pretty sure something's wrong because I'm not getting the number of edges I expect.) I'd be grateful for any help or direction. Thanks, Matthew -- 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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Single source shortest Path
by Christopher Morris 17 Aug '15

17 Aug '15

Hi, given a vertex v, I want compute all shortest paths starting at v, i.e., I want a list of edge or vertex lists, or some kind of DAG. Of course this can be easily solved by Dijkstra's Algorithm, but Graph-Tools doesn't seem to provide the right interface for this problem. Any ideas? Best regards, Chris

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