August 2012 - graph-tool - archives.skewed.de

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

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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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Undefined symbol drawing function
by sasho.j.markov 20 Apr '15

20 Apr '15

Hi New to the graph-tool. Build it from src on Fedora 16 (64) . Built with cairomm enabled . Try to run as per the quick start , however when executing graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ... output_size=(200, 200), output="two-nodes.pdf") i get undefined symbol _ZN5Cairo7ContextC1EP6_cairob However the symbol above is defined in : libcairomm-1.0.so see below nm command results nm /usr/local/lib/libcairomm-1.0.so | grep -i _ZN5Cairo7ContextC1EP6_cairob 0000000000014b90 T _ZN5Cairo7ContextC1EP6_cairob Interestingly the library libgraph_tool_draw.so has indeed have the undefined symbol U _ZN5Cairo7ContextC1EP6_cairob but does not depend on the cairomm libarary - see the ldd output . unless the library is dynamically load i do not understand why Any advise appreciated- regards Sasho ldd /usr/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so linux-vdso.so.1 => (0x00007fffc46da000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f99fd6cd000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f99fd30e000) libboost_iostreams.so.1.49.0 => /usr/local/lib/libboost_iostreams.so.1.49.0 (0x00007f99fd0f6000) libboost_python.so.1.49.0 => /usr/local/lib/libboost_python.so.1.49.0 (0x00007f99fceaa000) libboost_regex.so.1.49.0 => /usr/local/lib/libboost_regex.so.1.49.0 (0x00007f99fcbc8000) libCGAL.so.9 => /usr/local/lib/libCGAL.so.9 (0x00007f99fc9a5000) libexpat.so.0 => /usr/local/lib/libexpat.so.0 (0x00007f99fc77c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f99fc54d000) libm.so.6 => /lib64/libm.so.6 (0x00007f99fc2c9000) libc.so.6 => /lib64/libc.so.6 (0x00007f99fbf11000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99fbcfb000) /lib64/ld-linux-x86-64.so.2 (0x00000030cea00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99fbadf000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f99fb8db000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f99fb6d7000) libz.so.1 => /lib64/libz.so.1 (0x00007f99fb4c0000) librt.so.1 => /lib64/librt.so.1 (0x00007f99fb2b8000) libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x00007f99fb0b3000) libboost_thread.so.1.49.0 => /usr/local/lib/libboost_thread.so.1.49.0 (0x00007f99fae98000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007f99fac41000) -- 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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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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(no subject)
by 任强 08 Oct '12

08 Oct '12

HI everyone! I have tried to install graph_tool by compiling source code.But for many times , it reports: virtual memory exhausted: Cannot allocate memory My PC has a 4G main memory and Intel i5 CPU.I thought 4G is enough. Then I tried to install by apt-get, and came up with a problem. I have already installed these library before, and versions are right. graph-tool : Depends: libboost-iostreams1.42.0 (>= 1.42.0-1) but it is not installable Depends: libboost-python1.42.0 (>= 1.42.0-1) but it is not installable Depends: libboost-regex1.42.0 (>= 1.42.0-1) but it is not installable Depends: libcgal5 but it is not installable Depends: libpython2.6 (>= 2.6) but it is not installable Depends: libboost1.42-dev but it is not installable Can anyone help me ? By the way,how to use the public key ? I have tried "apt-key add signature.asc",but it reports: gpg: no valid OpenPGP data found.

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Compiling graph-tool with boost 1.42, missing buffer_concepts.hpp
by steffen 05 Sep '12

05 Sep '12

Hi there, I have problems compiling the new version of graph-tool (2.2.17) on ubuntu 11.04. Previous version 2.2.15 worked fine. The compilation error says In file included from graph_minimum_cut.cc:22:0: ./../../boost-workaround/boost/graph/stoer_wagner_min_cut.hpp:15:43: fatal error: boost/graph/buffer_concepts.hpp: No such file or directory compilation terminated. and, indeed, I cannot find that file (buffer_concepts.hpp) in the boost-directories. I have installed boost 1.42 (ubuntu repositories). Is a newer version of boost required? Cheers, Steffen -- 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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Best Values for Community Structure?
by cc 31 Aug '12

31 Aug '12

I know this is probably a very simple question to answer for those on here, but what are, or how does one determine the optimal values for the community_structure algorithm (http://projects.skewed.de/graph-tool/doc/community.html#graph_tool.communit… I know that the documentation states a history_file is available for this purpose, which I understand, but I'm confused as to what I am supposed to look for? Is there a certain pattern over a number of iterations that shows an optimal fit? Sorry if this is a bit confusing, but I'm very curious with respect to a kind-of tutorial on how to take the community_structure algorithm, decide the input values (on the basis of something?), and then determine which values fit the graph (again, on the basis of something else). My next step is, of course, to analyse Reichardt and Bornholdt theoretically to try and make sense of what I need to look for in this algorithm to apply it to something. It looks like a very powerful algorithm, but the theoretical basics have me baffled. Thank you so much for your help! -- 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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Show Members of Community Condensation Graph
by mstcamus 11 Aug '12

11 Aug '12

Is it possible to show the members of the communities shown in the http://projects.skewed.de/graph-tool/doc/community.html#graph_tool.communit… condensation graph documentation. For example, I have a graph in GraphML that I import with the vertex property "_graphml_vertex_id", from which I follow the rest of the example posted in the documentation to produce a condensation graph. However, I want to see which vertices end up being grouped together. How would one go about reversing the condensation graph to see the groupings? I apologise if my question is silly, I'm still very new to graph-tool, which I think is a remarkable piece of work (thank you!). -- 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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Problems with graph drawing
by steffen 07 Aug '12

07 Aug '12

Hi again, I finally managed to compile the new version of graph-tool with the newest boost version. However, I had some issues installing all the required libraries (CGAL, cariomm, pycairo) correctly and quite a number warnings appeared during the compilation of graph-tool... (So, most probably it is my fault, that things are not working perfectly.) My problem concerns the new drawing functionality with cairo. When I call graph_draw(), the following error appears Exception AttributeError: "'GraphWindow' object has no attribute 'graph'" in <bound method GraphWindow.__del__ of <GraphWindow object at 0xa5e125c (graph_tool+draw+gtk_draw+GraphWindow at 0xab1a8c8)>> ignored Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/karalus/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py", line 623, in graph_draw nodesfirst, **kwargs) File "/home/karalus/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py", line 950, in interactive_window nodesfirst, update_layout, **kwargs) File "/home/karalus/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py", line 885, in __init__ nodesfirst, update_layout, **kwargs) File "/home/karalus/lib/python2.7/site-packages/graph_tool/draw/gtk_draw.py", line 288, in __init__ self.connect("draw", self.draw) TypeError: <GraphWidget object at 0xaaf04dc (graph_tool+draw+gtk_draw+GraphWidget at 0xaa828d0)>: unknown signal name: draw Can you tell from this what is going wrong? Where should I look for the error? Cheers, Steffen -- 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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