graph-tool September 2015

graph-tool@skewed.de

10 participants
25 discussions

Simple Cycle Finder
by tanzairatier 25 Mar '16

25 Mar '16

Hello all, I'm wondering if anyone can suggest a strategy for finding elementary cycles with Graph-Tool. I'm working also with Network X, and they have a function for this, called simple_cycles(G). That function essentially runs Tarjan's Algorithm to find all strongly connected components, and then detects cycles within each of those components (this approach is called Johnson's Algorithm). I've tried to port the Network X code to Graph-Tool, but there are un-matching parallels in the data structures of both tools. e.g. Graph-Tool prefers to label with property maps. Since I've only begun using Graph-Tool a short while ago, this task is difficult for me. Any help would be appreciated, 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.

3 2

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

3 3

Bug in find_vertex_range?
by Santiago Videla 30 Sep '15

30 Sep '15

Hi, I updated graph-tool to 2.9 and I got an exception from find_vertex_range method (see below). Can you confirm this is a bug? ================ In [1]: import graph_tool.all as gt In [2]: g = gt.Graph() In [3]: g.add_edge_list([(0,1),(0,2),(1,2)]) In [4]: g.degree_property_map("out").a Out[4]: PropertyArray([2, 1, 0], dtype=int32) In [5]: gt.find_vertex_range(g,g.degree_property_map("out"),(2,3)) --------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-5-e6f941427c2a> in <module>() ----> 1 gt.find_vertex_range(g,g.degree_property_map("out"),(2,3)) /usr/lib/python2.7/dist-packages/graph_tool/util/__init__.pyc in find_vertex_range(g, prop, range) 65 ret = libgraph_tool_util.\ 66 find_vertex_range(g._Graph__graph, _degree(g, prop), ---> 67 (_convert(prop, range[0]), _convert(prop, range[1]))) 68 return ret 69 NameError: global name '_convert' is not defined ================ Regards, -- Santiago Videla http://www.linkedin.com/in/svidela

2 1

graph_tool.topology.shortest_distance on reversed graph yields a RuntimeError
by François 28 Sep '15

28 Sep '15

Hi, I've updated form 2.7 to '2.8 (commit e523cea5, Sun Sep 27 11:17:31 2015 +0200)'. Since the update *graph_tool.topology.shortest_distance* applied to a *reversed* graph yields a *RuntimeError*. You'll find below the steps to reproduce the bug. In order to have a fallback solution, would it be possible to keep latest version(s) of the package available on the repository ? >>> g=gt.Graph(directed=True) >>> g.add_vertex(3) <generator object <genexpr> at 0x7f7d1bb1a550> >>> g.add_edge(1,2) <Edge object with source '1' and target '2' at 0x7f7d256beb98> >>> g.add_edge(0,1) <Edge object with source '0' and target '1' at 0x7f7d256beb00> >>> g <Graph object, directed, with 3 vertices and 2 edges at 0x7f7d256d5ad0> >>> shortest_distance(g, source=1, target=2, pred_map=True) (1, <PropertyMap object with key type 'Vertex' and value type 'int64_t', for Graph 0x7f7d256d5ad0, at 0x7f7d256e3cd0>) >>> shortest_distance(gt.GraphView(g, reversed=True), source=1, >>> target=2,pred_map=True) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 1256, in shortest_distance pmap = g.copy_property(u.vertex_index, value_type="int64_t") File "/usr/lib/python2.7/dist-packages/graph_tool/decorators.pyc", line 2, in copy_property Vc File "/usr/lib/python2.7/dist-packages/graph_tool/decorators.py", line 144, in wrapper return f(*args, **kwargs) File "/usr/lib/python2.7/dist-packages/graph_tool/decorators.pyc", line 2, in copy_property Vc File "/usr/lib/python2.7/dist-packages/graph_tool/decorators.py", line 144, in wrapper return f(*args, **kwargs) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 2168, in copy_property _prop("v", self, tgt)) RuntimeError -- 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.

3 5

Segmentation fault when running the animation scripts in the Cookbook section
by yannis panagis 26 Sep '15

26 Sep '15

Dear all, I am new to graph tool. I have installed it under Ubuntu 14.04 64-bit and Python 2.7. When I tried to run the animation demos in the Cookbook section of the documentation I got a segmentation fault error. I loaded the core with gdb but couldnt get any further details on the source of the error. Stepping into the code I managed to find out that the segmentation fault takes place when win.graph.regenerate_surface() is executed, e.g. On line 122 in animation_sirs.py. Gtk seems to be using TkAgg for what it matters. Do you have any idea on why this error occurs? Shall I try another GTK backend? Kind regards Yannis

3 6

SNAP vs. Graph-tools
by Christopher Morris 26 Sep '15

26 Sep '15

Hi, does anybody have experience how Graph-tool compares to the Python interface of SNAP [1] performance-wise? Best regards, Chris [1] http://snap.stanford.edu/snappy/index.html

2 1

Deciding if vertex is in subgraph
by Christopher Morris 25 Sep '15

25 Sep '15

Hi, given a graph G and a subgraph S of G (computed using GraphView). What is the best way to check if a vertex v in V(G) is also in V(S). Is there are better way than iterating over all vertices in S? Best regards Chris

3 3

Obtaining a vertex or edge induced subgraph
by Christopher Morris 18 Sep '15

18 Sep '15

Hi, given a graph G, I want to traverse G in some way, e.g., a random walk of length k, resulting in a set S of vertices or edges. What is the fastest way of retrieving the subgraph of G induced by S. Is there a better way than using a property map and then GraphView? Best regards Christopher

2 2

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 September 2015