graph-tool June 2011

graph-tool@skewed.de

5 participants
14 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

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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

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Feature request: "Personalized" PageRank
by Anders Johannsen 27 Jun '11

27 Jun '11

Hi, Thank you for a providing this great library. The convenience of Python and the speed of native code really is a happy marriage. I'm missing one thing though. It would be great if you could bias the random jump vector for the PageRank algorithm. This modification is called "personalization". By providing non-uniform jump probabilities you selectively downplay or raise the importance of certain nodes. In natural language processing, where I work, this trick has quite a few applications. For reference, the parameterization is implemented in NetworkX [1]. Unfortunately, it becomes very slow once the graphs get large. Thanks, Anders Johannsen [1] http://networkx.lanl.gov/reference/generated/networkx.algorithms.link_analy…

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graph-tool problems with gcc 4.4.5 on ubuntu
by Sebastian Weber 27 Jun '11

27 Jun '11

Hi! I am on ubuntu 10.10 and trying to compile git version of graph-tool with gcc 4.4.5 and I get this error: CXX graph_properties_copy.lo In file included from /home/sweber/.local/include/boost/python/detail/wrap_python.hpp:50, from /home/sweber/.local/include/boost/python/detail/prefix.hpp:13, from /home/sweber/.local/include/boost/python/extract.hpp:8, from graph_properties_copy.cc:19: /usr/local/include/python2.7/pyconfig.h:1149: warning: "_POSIX_C_SOURCE" redefined /usr/include/features.h:162: note: this is the location of the previous definition /usr/local/include/python2.7/pyconfig.h:1171: warning: "_XOPEN_SOURCE" redefined /usr/include/features.h:164: note: this is the location of the previous definition /home/sweber/.local/include/boost/mpl/aux_/preprocessed/gcc/bind_fwd.hpp: In member function ‘void graph_tool::GraphInterface::CopyVertexProperty(const graph_tool::GraphInterface&, boost::any, boost::any)’: /home/sweber/.local/include/boost/mpl/aux_/preprocessed/gcc/bind_fwd.hpp:18: error: ‘template<class F, class T1, class T2, class T3, class T4, class T5> struct boost::mpl::bind’ is not a function, /home/sweber/.local/include/boost/bind/bind.hpp:1728: error: conflict with ‘template<class A1, class M, class T> boost::_bi::bind_t<typename boost::_bi::dm_result<M T::*, A1>::type, boost::_mfi::dm<M, T>, typename boost::_bi::list_av_1<A1>::type> boost::bind(M T::*, A1)’ graph_properties_copy.cc:122: error: in call to ‘bind’ /home/sweber/.local/include/boost/mpl/aux_/preprocessed/gcc/bind_fwd.hpp: In member function ‘void graph_tool::GraphInterface::CopyEdgeProperty(const graph_tool::GraphInterface&, boost::any, boost::any)’: /home/sweber/.local/include/boost/mpl/aux_/preprocessed/gcc/bind_fwd.hpp:18: error: ‘template<class F, class T1, class T2, class T3, class T4, class T5> struct boost::mpl::bind’ is not a function, /home/sweber/.local/include/boost/bind/bind.hpp:1728: error: conflict with ‘template<class A1, class M, class T> boost::_bi::bind_t<typename boost::_bi::dm_result<M T::*, A1>::type, boost::_mfi::dm<M, T>, typename boost::_bi::list_av_1<A1>::type> boost::bind(M T::*, A1)’ graph_properties_copy.cc:133: error: in call to ‘bind’ make[4]: *** [graph_properties_copy.lo] Error 1 make[4]: Leaving directory `/home/sweber/libs/graph-tool/src/graph' BTW, the git archive on skewed is not working for me any more. I have to use one of the other mirrors. My boost version is 1.46.1. If this is not trivial to solve, I just skip to gcc 4.5 which is also available on this platform. Cheers, -- 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

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GraphViews of GraphViews??
by Sebastian Weber 22 Jun '11

22 Jun '11

Hi! I am trying to subset my graph to a smaller graph which I do by making a view of the original graph. Then from that graph I want to keep the largest component. Hence, I do another GraphView of that former GraphView. This does for some reason not work. Aren't graph view supposed to work on graph views themselfes. The solution which is now working for me is: gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = label_largest_component(gp) path_lc = [] for v in gp.vertices(): if(gpl[v]): path_lc.append(int(v)) The more elegant solution gPath_ind = [ eg2id[e] for e in egPath ] gPath_filt = g.new_vertex_property("bool") gPath_filt.a[:] = False gPath_filt.a[gPath_ind] = True gp = GraphView(g, vfilt=gPath_filt) gpl = GraphView(gp, vfilt=label_largest_component(gp)) path_lc = [ int(v) for v in gpl.vertices() ] fails for some reason I don't see. BTW, in the end I want the vertex indices in the very original graph, which is what I hope to get here, but I am not really sure about that as I could not find anything about how to obtain vertex identifiers of filtered graphs which are good for referring to nodes in the original un-filtered graph. Or I overlooked it somewhere... BTW, the newest graph-tool seems to compile and install just fine on MacOS. At least it brings its own DLFCN.py and hence installing out of the box. Cheers, -- 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

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Drawing properties (newbie question)
by Gustav 16 Jun '11

16 Jun '11

Hello, I'm a newcomer to Python and I don't understand the way I could get drawn some properties for edges or vertices. The documentation says: vprops : dict (default: {}) Additional vertex properties, as a dictionary. The keys are the property names, and the values must be convertible to string, or vertex property maps, with values convertible to strings. But I guess that I'm missing something with Python as I only get drawn a text description of the object. Foe example: If I try a sentence like graph_draw(g, eprops={"label": g.edge_properties}, output="two-nodes2.png") it draws obviously the label for that object which is: {'occ': <PropertyMap object with key type 'Edge' and value type 'int32_t', for Graph 0x2f6dcd0, at 0x2f6de10>} But I don't understand which parameter I should pass to graph_draw in order to get the desired outcome. Could you provide a mini-example of drawing a small graph with properties on edges/vertices? This could also be added to the Quick tutorial. Thank you in advance peers. Regards. -- 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 and Macports
by Sebastian Weber 16 Jun '11

16 Jun '11

Hi there! To answer my previous question myself: The trouble with dl and the like ceases once one creates a DLFCN.py file via the h2py.py script inside the python 2.7 source distribution. This file must be kept somewhere reachable to python - for example in the graph-tool python directory. Morever, I fixed the problem with the wrong installation paths in the Portfile. As a result I obtained a fully working graph-tool inside macports. Note, that I compile numpy and scipy with the apple gcc which is not the default in Macports. When loading graph-tool, I get though this error: Traceback (most recent call last): File "../../python/grid2gml.py", line 3, in <module> from graph_tool.all import * File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/all.py", line 31, in <module> from graph_tool.draw import * File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/draw/__init__.py", line 69, in <module> libc.open_memstream.restype = ctypes.POINTER(ctypes.c_char) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 366, in __getattr__ func = self.__getitem__(name) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 371, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(RTLD_DEFAULT, open_memstream): symbol not found This seems to relate to new changes in git. Included is the Portfile I used which now has openmp disabled by default, since this will crash the apple gcc anyway... Cheers, -- 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

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graph-tool still compiles
by Sebastian Weber 14 Jun '11

14 Jun '11

Hi! The openmp variant should be deleted from the Portfile which I am just using to compile graph-tool. The apple gcc does not like openmp and prefers to crash instead of properly compiling... So forget about my previous post. CU, -- 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

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Compilation of git version not working at the moment with gcc 4.2 on apple
by Sebastian Weber 14 Jun '11

14 Jun '11

Hi! Some changes coming from the last changeset in git appear to smash the apple compiler for some reason: :info:build graph_geometric.hh: In member function 'void graph_tool::get_geometric::operator()(Graph&, Pos, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::pair<double, double>, std::allocator<std::pair<double, double> > >&, double, bool) const [with Graph = boost::UndirectedAdaptor<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, long unsigned int, boost::no_property>, boost::no_property, boost::listS> >, Pos = boost::unchecked_vector_property_map<std::vector<double, std::allocator<double> >, boost::vec_adj_list_vertex_id_map<boost::no_property, long unsigned int> >]': :info:build graph_geometric.hh:163: internal compiler error: in lower_stmt, at gimple-low.c:286 :info:build Please submit a full bug report, :info:build with preprocessed source if appropriate. :info:build See <URL:http://developer.apple.com/bugreporter> for instructions. :info:build make[4]: *** [graph_geometric.lo] Error 1 :info:build make[4]: *** Waiting for unfinished jobs.... :info:build make[3]: *** [all-recursive] Error 1 :info:build make[2]: *** [all-recursive] Error 1 :info:build make[1]: *** [all-recursive] Error 1 :info:build make: *** [all] Error 2 Any idea? Cheers, -- 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

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graph-tool June 2011