graph-tool May 2012

graph-tool@skewed.de

9 participants
13 discussions

graph-tool can't find Graphviz renderer
by Mikhail Spivakov 07 Apr '16

07 Apr '16

Hello! I've got graphviz installed with python and python27 bindings. However, when I do: graph_draw(ug, vprops={"label": ug.vertex_index}, output="two-nodes.pdf", layout="fdp") I get the following error: graph G { graph [outputorder=edgesfirst, mode=major, overlap=true, ratio=fill, size="5.905512,5.905512", start=3019255687130444316]; node [label="\N", shape=circle, width="0.105", height="0.105", style=filled, color="#2e3436", fillcolor="#a40000"]; edge [arrowsize="0.3", color="#2e3436", penwidth="1.0"]; graph [bb="0,0,425,425"]; 0 [label=0, width="0.47", height="0.47", pos="330,101"]; 1 [label=1, width="0.47", height="0.47", pos="93,324"]; 0 -- 1 [pos="318,113 277,152 147,274 106,312"]; } Error: renderer for pdf is unavailable Out[8]: <PropertyMap object with key type 'Vertex' and value type 'vector<double>', for Graph 0x5ff3f90, at 0x6001290> At the same time, if I save the above dot expression as test1.dot and run the following command from the command line: $ dot -Tpng test1.dot -o graph1.png I get a beautiful graph1.png. Graphviz is installed in a non-standard location as I don't have admin rights. However, the graphviz folder is in LD_LIBRARY_PATH and gv.py is in PYTHONPATH. Would very much appreciate your advice on what else graph-tool might need to find the libraries and/or how to test it better. Many thanks, Mikhail

3 5

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

3 7

how to use a python object saved in a graph property map
by Héctor Urbina 03 Jun '12

03 Jun '12

Hello, I have the following code: sortedEdges = [] g = Graph() g.graph_properties["sortedEdges"] = self._graph.new_graph_property("object", sortedEdges) then I fill the sortedEdges list with the appropriate values and return g. Now, how can I get the list of sorted edges from g? I'm also saving a dictionary that uses the names of the vertices as keys and the graph vertices as values in a internal graph property map; so, in general, I want to learn how to use any python object after it is saved as graph_property Thanks, -- Héctor Urbina S. Ingeniero en Bioinformática Fono: 82049138

2 1

max flow min cut
by BWIND 03 Jun '12

03 Jun '12

hi, I'm relatively new to Python but i managed to get the build the graph and attach the capacities to the edges and got some results from the Maxflow algorithm. I what to used to implement the min cut and separate the graph in two. Did anybody tried this? Bernardo Mota

2 1

bridge detection in graph-tool
by Peng Yu 29 May '12

29 May '12

Hi, I'm not able to find a bridge detection algorithm implemented in graph-tool. In case that I missed anything, could anybody confirm with me whether there is an implementation available? -- Regards, Peng

2 1

Installing graph-tool using pip
by Peng Yu 24 May '12

24 May '12

Hi, I don't see a way to install graph-tool using pip. Port on Mac OS X is not updated as frequently as pip. I'd recommend adding a way to install graph-tool using pip. Right now, I see the following error. /tmp$ pip install graph-tool Downloading/unpacking graph-tool Downloading graph-tool-2.2.15.tar.bz2 (520Kb): 520Kb downloaded Running setup.py egg_info for package graph-tool Traceback (most recent call last): File "<string>", line 14, in <module> IOError: [Errno 2] No such file or directory: '/private/tmp/build/graph-tool/setup.py' Complete output from command python setup.py egg_info: Traceback (most recent call last): File "<string>", line 14, in <module> IOError: [Errno 2] No such file or directory: '/private/tmp/build/graph-tool/setup.py' ---------------------------------------- Command python setup.py egg_info failed with error code 1 -- Regards, Peng

2 7

RuntimeError: Gtk couldn't be initialized
by Alasdair Macmillan 23 May '12

23 May '12

Hi there Just installed graph-tool for the first time & get this error. What does it mean? How can i fix? I'm on Ubuntu Server 12.04 Much appreciated Al >>> from graph_tool.all import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/graph_tool/all.py", line 31, in <module> from graph_tool.draw import * File "/usr/lib/python2.7/dist-packages/graph_tool/draw/__init__.py", line 589, in <module> from cairo_draw import graph_draw, GraphWidget, GraphWindow, \ File "/usr/lib/python2.7/dist-packages/graph_tool/draw/cairo_draw.py", line 59, in <module> from gi.repository import Gtk, Gdk, GdkPixbuf File "/usr/lib/python2.7/dist-packages/gi/importer.py", line 76, in load_module dynamic_module._load() File "/usr/lib/python2.7/dist-packages/gi/module.py", line 224, in _load overrides_modules = __import__('gi.overrides', fromlist=[self._namespace]) File "/usr/lib/python2.7/dist-packages/gi/overrides/Gtk.py", line 1517, in <module> raise RuntimeError("Gtk couldn't be initialized") RuntimeError: Gtk couldn't be initialized

2 2

Problem with new version on ubuntu oneiric
by Giuseppe Profiti 22 May '12

22 May '12

Hi all, I'm trying to install the new binary package but I'm having troubles with the dependency from libcairomm-1.0. I already have libcairomm-1.0-1 (version 1.10-0-1) installed, along with libcairomm-1.0-dev (installed while trying to solve this problem). Before installing the binary release I removed (via make uninstall) a custom build made from git sources. Any hint? I can't build it from source, because I run out of memory while compiling graph_sfdp.lo (even having 2GB of ram free before running make). Thanks in advance, Giuseppe

2 2

Re: [graph-tool] libcairomm1.0 dependency in debian squeeze [SOLVED]
by Rodrigo Agerri 22 May '12

22 May '12

Hi, Just to confirm that I could install and use graph-tool without any problems. Thanks, Rodrigo On Wed, May 16, 2012 at 1:06 PM, Tiago de Paula Peixoto <tiago(a)skewed.de> wrote: > Hi Rodrigo, > > > On 2012-05-16 12:58, Rodrigo Agerri wrote: >> >> Hi, >> >> I tried to install the graph-tool .deb package in debian squeeze from >> the following repository >> >> deb http://downloads.skewed.de/apt/squeeze squeeze main >> >> but I cannot solve a libcairomm.10 dependency: > > > > This is my fault. I built the packages with the wrong dependency. I'm > rebuilding all > the packages right now, and I'll update them in the server soon. Stay tuned. > > Cheers, > Tiago > > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > _______________________________________________ > graph-tool mailing list > graph-tool(a)skewed.de > http://lists.skewed.de/mailman/listinfo/graph-tool

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graph-tool May 2012