graph-tool January 2011

graph-tool@skewed.de

3 participants
4 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

3 7

Possible bug in flow?
by jeremy 14 Jan '11

14 Jan '11

Hi, I'm looking to use graph-tool for some work involving percolation theory. So far it is a clear preference over the alternatives (networkx, etc). BUT, I have just tried to use the max flow algorithms with the following result: File "/usr/lib/python2.7/site-packages/graph_tool/flow/__init__.py", line 238, in push_relabel_max_flow _prop("e", g, residual)) RuntimeError: No static implementation was found for the desired routine. This is a graph_tool bug. :-( Please follow but report instructions at http://graph-tool.skewed.de. What follows is debug information. Graph view: boost::UndirectedAdaptor<boost::filtered_graph<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, unsigned long, boost::no_property>, boost::no_property, boost::listS>, boost::keep_all, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::vec_adj_list_vertex_id_map<boost::no_property, unsigned long> > > > >* Action: boost::_bi::bind_t<void, get_push_relabel_max_flow, boost::_bi::list7<boost::arg<1>, boost::_bi::value<boost::adj_list_edge_property_map<boost::bidirectional_tag, unsigned long, unsigned long&, unsigned long, boost::property<boost::edge_index_t, unsigned long, boost::no_property>, boost::edge_index_t> >, boost::_bi::value<unsigned long>, boost::_bi::value<unsigned long>, boost::_bi::value<unsigned long>, boost::arg<2>, boost::arg<3> > > Arg 1: boost::checked_vector_property_map<double, boost::adj_list_edge_property_map<boost::bidirectional_tag, unsigned long, unsigned long&, unsigned long, boost::property<boost::edge_index_t, unsigned long, boost::no_property>, boost::edge_index_t> > Arg 2: boost::checked_vector_property_map<double, boost::adj_list_edge_property_map<boost::bidirectional_tag, unsigned long, unsigned long&, unsigned long, boost::property<boost::edge_index_t, unsigned long, boost::no_property>, boost::edge_index_t> > All of the max flow methods return this exception. Is there something wrong with my set-up? Or is this a genuine bug? Max flow is critical to my project and I would prefer not to sacrifice speed and use networkx. Thanks, Jeremy -- 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 3

Graph tool installation issues on SGI machine
by shankha 07 Jan '11

07 Jan '11

Hi, I am trying to install graph-tool on a SGI system. uname -a : Linux 2.6.16.60-0.69.1-default #1 SMP Fri Sep 17 17:07:54 UTC 2010 ia64 ia64 ia64 GNU/Linux Command line used : /home/arcadm/SGI/Software/graph-tool/graph-tool-2.2.9/configure --with-boost=/apps/packages/boost_1_45_0 --with-boost-libdir=/apps/packages/boost_1_45_0/lib --with-boost-python=/apps/packages/boost_1_45_0/lib/libboost_python.so --prefix=/apps/packages/graph-tool ENVIORNMENT VARIABLES: LDFLAGS=-L/apps/packages/boost_1_45_0/lib -L/apps/packages/cgal-3.6.1/lib CPPFLAGS=-I/apps/packages/boost_1_45_0/include -I/apps/packages/cgal-3.6.1/include -I/apps/packages/Python-2.6.6/include/python2.6 LD_LIBRARY_PATH=/apps/packages/cgal-3.6.1/lib:/apps/packages/RS:/apps/packages/taucs:/apps/packages/metis-4.0:/apps/packages/atlas-3.9.32/lib:/apps/packages/boost_1_45_0/lib:/apps/packages/gcc-4.4.4/lib:/apps/packages/mpfr-3.0.0/lib:/apps/packages/gmp-5.0.1/lib:/apps/packages/Python-2.6.6/lib I have made sure all the dependent libraries for graph-tool are taken care by the LD_LIBRARY_PATH. ERROR MESSAGE: checking for python2.6/Python.h... (cached) no results of the Python check: Binary: python2.6 Library: python2.6 Include Dir: no checking whether the Boost::Python library is available... no configure: error: No usable boost::python found config.log error message: configure:17155: checking for python2.6/Python.h configure:17155: result: no configure:17180: result: results of the Python check: configure:17182: result: Binary: python2.6 configure:17184: result: Library: python2.6 configure:17186: result: Include Dir: no configure:17198: checking whether the Boost::Python library is available configure:17228: g++ -c -Wall -ftemplate-depth-150 -Wno-deprecated -O99 -fvisibility=default -fvisibility-inlines-hidden -Wno-unknown-pragmas -I/apps/packages/Python-2.6.6/include/python2.6 conftest.cpp >&5 conftest.cpp:35:36: error: boost/python/module.hpp: No such file or directory conftest.cpp:36: error: 'boost' has not been declared conftest.cpp:36: error: 'python' is not a namespace-name conftest.cpp:36: error: expected namespace-name before ';' token conftest.cpp:37: error: expected constructor, destructor, or type conversion before '(' token configure:17228: $? = 1 I have attached config.log for your reference. python.h is installed in Python2.6/include/python2.6 and not Python2.6. I am not sure why it is searching for python.h in Python2.6. I can create a soft link inside Python2.6 to the actual file in Python2.6/include/python2.6 but I am not sure if that is the right way to go about it. Could you please help me out on this issue. -- Thanks Shankha Banerjee

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graph-tool January 2011