graph-tool December 2011

graph-tool@skewed.de

4 participants
7 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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about graph-tool and mac os x lion
by Martella, C. 31 Dec '11

31 Dec '11

Hello, I see recently many people have had one problem or another to run graph-tool on mac os x. I've been able to build graph-tool on Lion, with apple gcc 4.2, boost 1.47 and python 2.7.2 (these last two from homebrew). The problem is that graph_tool doesn't import: ImportError Traceback (most recent call last) /Users/hammer/TIS/java-hacking/giraph/<ipython-input-1-100bbe2bc9d9> in <module>() ----> 1 from graph_tool.all import * /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py in <module>() 89 import scipy.stats 90 ---> 91 from dl_import import * 92 dl_import("import libgraph_tool_core as libcore") 93 import libgraph_tool_core as libcore # for pylint /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/dl_import.py in <module>() 25 # handle strange python installations, by importing from the deprecated dl 26 # module ---> 27 from dl import RTLD_LAZY, RTLD_GLOBAL 28 29 __all__ = ["dl_import"] ImportError: No module named dl I noticed that DLFCN module is missing on my python install. I tried to substitute the RTLD_LAZY and RTLD_GLOBAL values (0x1 and 0x8) taken from the include file dlfcn.h into the setdlopenflags call in that same dl_import.py, but i get a trap back: Fatal Python error: Interpreter not initialized (version mismatch?) Abort trap: 6 Do you have any idea? How did you guys get graph_tool working on mac os? thanks! -- Claudio Martella claudio.martella(a)vu.nl

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current git version not working...
by Sebastian Weber 30 Dec '11

30 Dec '11

autogen.sh results in configure.ac:331: required file `src/graph/draw/Makefile.in' not found looking into it shows that there is no draw directory inside graph. Something not checked into git? 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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gml compilation issues
by Sebastian Weber 28 Dec '11

28 Dec '11

Hi! I just failed to compile the latest graph-tool svn with gml enabled. The log of the compiler is enclosed. My system is Mac OSX Lion, boost 1.47.0 python 2.7.1 from Apple, gcc 4.2 compiler The 2.2.15 version finished flawlessly to compile. BTW, what about the macports graph-tool port? Is it known to work? What compiler, which boost, and what python version is required? MacOS is a mess in this regard… 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 on MacOSX Lion
by Sebastian Weber 28 Dec '11

28 Dec '11

Hi! Anyone got graph-tool working on Lion? It was a real mess to set it up under Snow Leopard, and I am running into some issues again. Hence did someone make it work? Macports? Python version? scipy/numpy version? boost version? CGAL? Which compiler - the apple one? If Macports, what did you compile with which option? Thanks a lot for any hint here. 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 and boost 1.48 (mac os)
by Claudio Martella 12 Dec '11

12 Dec '11

Hi, I'm trying to build according to the linked homebrew Formula (but i also tried downloading the source and building straight ahead). I have llvm gcc 4.2 (mac os x standard) and boost 1.48. I get the following error pretty straight ahead at compile time (for graph_betweenness): /usr/local/include/boost/property_map/property_map.hpp:361: error: no match for 'operator[]' in '(const boost::unchecked_vector_property_map<double, 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::no_property>, boost::edge_index_t> >&)((const boost::unchecked_vector_property_map<double, 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::no_property>, boost::edge_index_t> >*)(& pa))[k]' ./../fast_vector_property_map.hh:170: note: candidates are: typename std::iterator_traits<typename std::vector<T, std::allocator<_CharT> >::iterator>::reference boost::unchecked_vector_property_map<T, IndexMap>::operator[](const typename boost::property_traits<IndexMap>::key_type&) const [with T = double, IndexMap = 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::no_property>, boost::edge_index_t>] preceded by a looong series of "instantiated from" etc. What am I doing wrong? Thanks -- Claudio Martella claudio.martella(a)gmail.com

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graph-tool December 2011