graph-tool September 2011

graph-tool@skewed.de

5 participants
6 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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How to get HTML labels ?
by Tim Day 26 Sep '11

26 Sep '11

Is there some trick needed to get graphviz's HTML labels working from graph-tool ? I've been making some nice svg plots from graph-tool setting the label/shape/URL/tooltip vertex properties, but now I want to be able to have multiple URL links from each node and HTML labels seem the obvious way to do this. I have an idea it ought to be as simple as setting the label strings to something like (simple test case) <<TABLE><TR><TD>left</TD><TD>right</TD></TR></TABLE>> (and this seems to work as expected used in a .dot file) but setting the same thing from graph-tool just gets me the the formatting reproduced verbatim (extra '<' '>'s included) in the graph labels. Is some sort of escaping needed (or do I need to bypass some escaping graph-tool is doing) ? Thanks for any help Tim Using graph-tool 2.2.15-1 & graphviz 2.26.3-5 on Debian squeeze.

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graphtool compile error on F15
by Justin Keogh 24 Sep '11

24 Sep '11

Hi folks, is anyone using graph-tool with Fedora 15? Using Fedora 15 (gcc version 4.6.0 20110603) compiling the stable release or the latest git fails for me: # uname -a Linux localhost.localdomain 2.6.40.4-5.fc15.x86_64 #1 SMP Tue Aug 30 14:38:32 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux using boost 1.46.0 ./configure --with-numpy=/usr/lib64/python2.7/site-packages/numpy --with-scipy=/usr/lib64/python2.7/site-packages/scipy make /usr/include/boost/graph/graph_traits.hpp:222:47: error: no type named 'graph_property_type' in 'const class boost::reverse_graph<boost::filtered_graph<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, long unsigned int> >, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::adj_list_edge_property_map<boost::bidirectional_tag, long unsigned int, long unsigned int&, long unsigned int, boost::property<boost::edge_index_t, long unsigned int>, boost::edge_index_t> > >, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::vec_adj_list_vertex_id_map<boost::no_property, long unsigned int> > > >, const boost::filtered_graph<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, long unsigned int> >, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::adj_list_edge_property_map<boost::bidirectional_tag, long unsigned int, long unsigned int&, long unsigned int, boost::property<boost::edge_index_t, long unsigned int>, boost::edge_index_t> > >, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::vec_adj_list_vertex_id_map<boost::no_property, long unsigned int> > > >&>' make[4]: *** [graph_trust_transitivity.lo] Error 1 make[4]: Leaving directory `/home/default/graph-tool/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/default/graph-tool/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/default/graph-tool/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/default/graph-tool' make: *** [all] Error 2 [user@localhost graph-tool]# full make log http://pastebin.com/raw.php?i=iJCDihKs Thank You, Justin

2 6

efficient way to load a numpy adjecency matrix?
by Matthias Ekman 23 Sep '11

23 Sep '11

Hi, sorry for my naive question. I'd like to import hundreds of large and dense adjacency matrices available as a numpy arrays into graph_tool. The following option takes very long. Q1: Is there a preferable alternative? import graph_tool.all as gt import numpy as np adj=np.array([[1,1,0],[1,1,0],[0,0,1]]) n_vertices=adj.shape[0] g = gt.Graph(directed=False) vlist = g.add_vertex(n_vertices) edge_ids = np.where(adj !=0) for i in range(edge_ids[0].shape[0]): g.add_edge(g.vertex(edge_ids[0][i]), g.vertex(edge_ids[1][i])) Since I am dealing with undirected graphs without selfloops a first step would be to take only one triangle of the symmetric adjacency matrix: # get ids of upper triangle upper_tr = np.triu_indices_from(np.zeros((n_vertices,n_vertices))) adj[a[0],a[1]] = 0 ... Q2: is this a valid approach? Thanks in advance, Matthias

2 1

Fast method for duplicated edge removal
by Giuseppe Profiti 22 Sep '11

22 Sep '11

Hello, I'm using a cvsreader to parse a very big file and create an undirected graph accordingly. The file can contain duplicated edges (i.e. A B in one row, B A in another one), so I'm checking if g.edge(v1,v2)==None: e = g.add_edge(v1,v2) in order to discard them (v1 and v2 are vertices created from what it's read from the file). However the graph contains a lot of edges (few millions) and vertices (many thousands), with a potentially high degree for the vertices, and it takes a lot to process the data. As far as I read in the soruce code, the Graph.edge() method checks all the outgoing edges of the source node, but even if I check which node has the highest degree, it takes a lot of time to build the graph. Is there any other way to remove the duplicated edges? Maybe an edge filter based on some lambda wizardry? Thanks in advance, Giuseppe -- Researcher at University of Bologna, Italy

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graph-tool September 2011