graph-tool March 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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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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graph-tool installing and cygwin
by dd 02 Apr '11

02 Apr '11

Hi to all, I'm trying to configure, build and install graph-tool in a windows environment using CygWin. I already successfully installed all the dependencies reported in the graph-tool website. The problem arises while running "configure" script: when it tries to find a python version it comes to me the following error: checking for python... (cached) /cygdrive/c/Program Files/Python27/python checking for a version of Python >= '2.1.0'... configure: line 16603: /cygdrive/ c/Program: No such file or directory no configure: error: in `/cygdrive/c/Program Files/graph-tool-2.2.11': configure: error: This version of the AC_PYTHON_DEVEL macro doesn't work properly with versions of Python before 2.1.0. You may need to re-run configure, setting the variables PYTHON_CPPFLAGS, PYTHON_LDFLAGS, PYTHON_SITE_PKG, PYTHON_EXTRA_LIBS and PYTHON_EXTRA_LDFLAGS by hand. Moreover, to disable this check, set PYTHON_NOVERSIONCHECK to something else than an empty string. See `config.log' for more details I guess the problem is with my python root directory, that is "C:\Program Files\Python27" and contains a blank space, so when the script receives from the cygwin environment the path "/cygdrive/c/Program Files/Python27" it searches for "/cygdrive/c/Program" that doesn't exist. I don't know if my supposition is correct... in any case, can anybody please help me to deal with this problem? Thanks in advance, DD -- 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 10

Query regarding graph layout in graph-tool
by kapil gupta 19 Mar '11

19 Mar '11

Hi All, I am very new to graph-tool and looking into its documentation. I've been playing with the F-R algorithm with weighted edges to layout time series data. I want to know is it possible in graph-tool to nominate a node to be the centre of the graph and have the layout chose the distance of near by nodes to be directly proportional to the strength of the edge weight. The more two nodes correlate, the closer together they are. Any help is appreciated. Thanks, Kapil PS: If graph-tool is not yet capable of nominating/fixing a particular node, is there any other python graph package which can do so? -- Kapil Gupta Phone: +91-9312505395 Alt Email: kapilgupta.iit(a)gmail.com

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parallel processing
by Sebastian Weber 16 Mar '11

16 Mar '11

Hi! I am intending to use the Parallel construct from the joblib library which basically runs an embarassingly parallel for loop via the multiprocessing facility. The error I get is Traceback (most recent call last): File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/threading.py", line 522, in __bootstrap_inner self.run() File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/threading.py", line 477, in run self.__target(*self.__args, **self.__kwargs) File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/multiprocessing/pool.py", line 225, in _handle_tasks put(task) RuntimeError: Pickling of "graph_tool.libgraph_tool_core.Vertex" instances is not enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) I thought graph-tool graphs are compatible with Python pickle-stuff - or do I have to watch out somewhere? Thanks for the help, -- 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

2 1

bug in graph_draw?
by Sebastian Weber 11 Mar '11

11 Mar '11

Hey, I am using the latest graph-tool 2.2.11, and this happens to stop working: Traceback (most recent call last): File "../python/mfptTest.py", line 40, in <module> graph_draw(G, layout="sfdp", output=graphName + ".pdf", eprops = {'arrowsize': 1.0, 'penwidth': Ecap }) File "/Volumes/Data/sebi/.local/lib/python2.6/site-packages/graph_tool/draw/__init__.py", line 274, in graph_draw gvg = gv.graph("G") NameError: global name 'gv' is not defined Inspecting the respective file reveals that gv is indeed not defined... Typo? 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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graph-tool March 2011