graph-tool August 2011

graph-tool@skewed.de

6 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

5 9

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

3 7

Using Inline for Search/Traversal
by parvizp 25 Aug '11

25 Aug '11

Is it possible to write the code for graph traversal in C++ rather than using the Python wrappers? I need the graph search to be as fast as possible. I tried something simple like this: http://pastebin.com/m2pwFQKy It looks like the typedefs for 'graph_graph_t' don't appear until after the support code: http://pastebin.com/itT73DxT Is there an example of how to achieve something similar? Thanks Tiago Peixoto for developing/maintaining this great library! -- 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.

2 1

elaboration please: remove_vertex_if&find_vertex
by tamo 14 Aug '11

14 Aug '11

Hi, Thank you again for this great library. First, could you please describe more details about using remove_vertex_if and find_vertex? and how to deal with the returned of those functions? also, I have a simulation scenario where I have to remove nodes with the 10 % highest degrees. thus, I tried to use the following code as initial attempt *prop = gt.find_vertex(g,"total",6) gv = gt.GraphView(g, vfilt=prop, efilt=None, directed=False, reversed=False) * but it shows me the following error Traceback (most recent call last): File "test-failure.py", line 57, in <module> gv = gt.GraphView(g, vfilt=gt.find_vertex(g,"total",6), efilt=None, directed=False, reversed=False) File "/usr/local/lib/python2.6/dist-packages/graph_tool/__init__.py", line 1525, in __init__ vmap[v] = vfilt(v) TypeError: 'list' object is not callable any help to do my scenario would be greatly appreciated Thank you 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.

2 5

Graph drawing: overlay possible?
by Sebastian Weber 11 Aug '11

11 Aug '11

Hi! I was wondering if it is possible to overlay two drawings of the same graph where I use different color-coded vertex sizes? Theses colors would need to be transparent and the graph layout must match in each drawing. Is there an easy way of doing so with graph-tool? Thanks! Regards, -- 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

3 9

Functions producing small-world / scale free / ER networks
by mehdi 06 Aug '11

06 Aug '11

Hi all, I would like to know if somebody has already coded functions for creating some small-world / scale free / ER networks with the following parameters (similar to networkx): small-world -> n : The number of nodes , k : Each node is connected to k nearest neighbors in ring topology , p: The probability of rewiring each edge scale-free -> n : Number of nodes, m : Number of edges to attach from a new node to existing nodes ER -> n : The number of nodes , p : Probability for edge creation. Cheers! Mehdi -- 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 August 2011