January 2013 - 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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Problem importing on Mac OS X 10.8, installed using MacPorts
by Uldis Bojars 07 Mar '14

07 Mar '14

Hi, When trying to import graph-tool the following error message is returned: >>> from graph_tool.all import * Fatal Python error: PyThreadState_Get: no current thread Could you help me solve this problem? graph-tool version py-graph-tool-2.2.18 was successfully installed using MacPorts but it fails during importing. Thanks, Uldis

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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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Extracting vertex subgraphs (based on property map)?
by Uldis Bojars 06 Feb '13

06 Feb '13

Hi, Could you suggest what is the most efficient way for: 1) extracting vertex clusters based on values in vertex property map? - e.g., for iterating through all connected components in a graph, based on result of label_components 2) saving extracted subgraphs to a file? Code that I am using is in [1] but for a large graph (~1M edges, 12k clusters) it is taking days. Is there a more optimal way? Can the function topology.mark_subgraph be of help here? - the name seems relevant but I do not know how it is used. [1] https://gist.github.com/4627494 - function save_all_graphs is called to save all the subgraphs Many thanks, Uldis

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Problem with ./configure and Boost::Python
by josh.columbus.chang＠gmail.com 30 Jan '13

30 Jan '13

Hi, I'm trying to install graph_tool on Centos 5.8 in a custom Python 2.7.2 environment. I have boost installed under /scratch/usr Running the following: ./configure --with-boost=/scratch/usr I get the error messages: graph-tool will be installed at: /scratch/opt/pythonbrew/pythons/Python-2.7.2/lib/python2.7/site-packages =========================== Using python version: 2.7.2 =========================== checking for boostlib >= 1.38.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... no checking for exit in -lboost_python-py2.7... no checking for exit in -lboost_python-2.7... no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python-py2.7... (cached) no checking for exit in -lboost_python-2.7... (cached) no checking for exit in -lboost_python-mt... no checking for exit in -lboost_python-mt-py2.7... no checking for exit in -lboost_python-mt-2.7... no configure: error: No usable boost::python found Is there something wrong with my boost installation? Thanks

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All-pairs-shortest-paths for unweighted and undirected graphs
by Sirius Fuenmayor 30 Jan '13

30 Jan '13

If I understand correctly the Floyd-Warshall and Johnson’s algorithms are only useful in weighted graphs, so I was looking for algorithms to compute the all-pairs-shortest-paths for unweighted and undirected graphs fastest than the usual breadth-first search (BFS) method, and I found these algorithms: Timothy M. Chan: All-pairs shortest paths for unweighted undirected graphs in o(mn) time. SODA 2006: 514-523 (https://www.waset.org/journals/ijcms/v3/v3-5-43.pdf) Raimund Seidel: On the All-Pairs-Shortest-Path Problem in Unweighted Undirected Graphs. J. Comput. Syst. Sci. 51(3): 400-403 (1995) ( www.mimuw.edu.pl/~mucha/teaching/alp2006/seidel92.pdf) Do you think it is plausible and possible to implement these algorithms? Any one have seen an implementation of these in any familiar language?

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Install graph-tool locally
by Adelbert Chang 25 Jan '13

25 Jan '13

Hello, I was wondering if it is possible to install graph-tool locally (I don't have pseudo access on the server and I'd rather not have to bug IT about it)? lf I install the dependencies (Boost, Expact, CGAL, etc.) locally (I have NumPy and Matplotlib installed locally already) can I point the install to those folders? Also, how can I upgrade graph-tool when a new release is made, or how can I uninstall/re-install a new version? Thanks! Regards, -Adelbert

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Compiling error: 'transform_iterator' does not name a type
by VaSa 18 Jan '13

18 Jan '13

I tried to build graph-tool from the latest source on Ubuntu 12.04 server (x64) and after getting packages required by ./configure --enable-openmp I've run into a compile error gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 dpkg -s libboost-dev | grep 'Version' Version: 1.48.0.2 Python 2.7.3 make all-recursive make[1]: Entering directory `/home/val/graph_tool_mp' Making all in src make[2]: Entering directory `/home/val/graph_tool_mp/src' Making all in graph make[3]: Entering directory `/home/val/graph_tool_mp/src/graph' Making all in centrality make[4]: Entering directory `/home/val/graph_tool_mp/src/graph/centrality' CXX graph_betweenness.lo In file included from ./../graph_filtering.hh:51:0, from graph_betweenness.cc:18: ./../graph_adaptor.hh:139:13: error: 'transform_iterator' does not name a type ./../graph_adaptor.hh:171:13: error: 'transform_iterator' does not name a type ./../graph_adaptor.hh:179:13: error: 'transform_iterator' does not name a type ./../graph_adaptor.hh: In instantiation of 'boost::transformed_out_range<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::no_property, boost::property<boost::edge_index_t, long unsigned int> > >': and about 5MB worth of error messages follow :) I could not find an exact match for this error on Google, except a possible need for some forward includes. If there is a suitable package with OpenMP support available somewhere for 12.04 that would be a great alternative to compiling oneself. The Precise repo for 12.04 (from http://downloads.skewed.de/apt/precise/) works great, but as far as I can tell, does not include OpenMP support(running algorithms only utilize one core). -- 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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