graph-tool July 2012

graph-tool@skewed.de

5 participants
11 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

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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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No usable boost::python found -- but
by Edward Newell 20 Jul '12

20 Jul '12

Hi, I'm trying to install graph-tool, but when running the configure script am getting this error "configure: error: No usable boost::python found" However I installed boost and went through the necessary steps to compile the boost-python portion of the library. The procedure to compile the boost-python portion of the library ends with a test, and this test is passed with no errors. All went as expected with boost and seemed right. I think I might know why the configure script might not be finding the boost library, though not sure what to do about it. I'm running Ubuntu 12.04, which comes with python2.7. However, I have installed the enthought python distribution, and this is what I associated boost-python to during its compilation. My guess is that this might have to do with the configure script finding the python that came bundled with my Ubuntu distribution, and not the Enthought python to which boost-python is associated. Would anyone be able to advise on how to proceed? Is there a way to tell it the path to the correct python installation? I also tried installing using apt-get. The installation seems to go well, but it associates to the version of python that came with my Ubuntu distribution, not Enthought python. I don't believe I can alter the behavior of apt-get. I need this to work with my Enthought python. Any hints would be much appreciated. Regards, -- Edward Newell

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Problems using the dijktstra search
by josubg 16 Jul '12

16 Jul '12

Hi all. I'm trying to use the dijktstra search But I have a exception.The property that is used a int32_t and the GraphViews aren't empty. Any clue of what is my error? This is the code: referents_graph = GraphView(graph, vfilt= lambda v: graph.vertex_properties["type"][v]=="referent") navigable_graph = GraphView(graph, reversed=True) referents = referents_graph.vertices() weight = navigable_graph.edge_properties["weight"] for base_referent in referents: # Calculate the distance of all accessible referents distances, predecessors = graph_tool.search.dijkstra_search(navigable_graph,base_referent,weight) This is the trace: File "/data/workspace/stanford-corenlp-python/contextgenerator.py", line 218, in resolve_corefenrence distances, predecessors = graph_tool.search.dijkstra_search(navigable_graph,base_referent,weight) File "/usr/local/lib/python2.7/dist-packages/graph_tool/decorators.pyc", line 2, in dijkstra_search Bq�Oc File "/usr/local/lib/python2.7/dist-packages/graph_tool/search/__init__.py", line 126, in wrap ret = func(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/graph_tool/search/__init__.py", line 841, in dijkstra_search compare, combine, zero, infinity) TypeError: No registered converter was able to produce a C++ rvalue of type int from this Python object of type float Thanks for the time. -- 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 4

find_vertex() not works
by josubg 11 Jul '12

11 Jul '12

I'm trying to retrieve all the nodes of a graph that belong to a specific type. I use the find_vertex for this: referents = find_vertex(graph, graph.vertex_properties['type'], 'referent') But all I get is this error: File "/usr/lib/python2.7/dist-packages/graph_tool/util/__init__.py", line 58, in find_vertex (val, val)) TypeError: No registered converter was able to extract a C++ reference to type graph_tool::GraphInterface from this Python object of type Graph. Any clue of what is the problem? -- 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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Get all the dependant nodes or a root node in a new sub-graph
by josubg 09 Jul '12

09 Jul '12

Hi everybody, I have a graph that contains all the word of a text. This graph is a a directed acyclic graph. I want to reconstruct sequences of this text so I need to get all the nodes and edges that are dependent of a root node or their children. In other words I want a Sub-tree of a tree. I cant get it with a recursive ad-hoc function, using out_neighbours(), but I am wondering if there is another more efficient way to obtain it. I searched in the doc but i don't find it. thanks. -- 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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Re: [graph-tool] graph-tool Digest, Vol 54, Issue 3
by Qiang Ren 05 Jul '12

05 Jul '12

How about the CGAL path? The error is : ImportError: libCGAL.so.9: cannot open shared object file: No such file or directory. My CGAL path is /usr/local/lib/ ,but I don't know the name of CGAL environment variable. 2012/7/2 <graph-tool-request(a)skewed.de> > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. Re: graph-tool Digest, Vol 54, Issue 1 (Tiago de Paula Peixoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 02 Jul 2012 11:47:34 +0200 > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: Main discussion list for the graph-tool project > <graph-tool(a)skewed.de> > Subject: Re: [graph-tool] graph-tool Digest, Vol 54, Issue 1 > Message-ID: <4FF16E36.9000809(a)skewed.de> > Content-Type: text/plain; charset="utf-8" > > On 07/02/2012 10:50 AM, Qiang Ren wrote: > > Hi ,all > > I finished installing graph_tool in Arch linux. > > There exists directory > /usr/local/lib/python2.7/site-packages/graph_tool. > > It seems right but I still can't import graph_tool. > > The message "File "<stdin>",line 1 in <module> ImportError: No module > named graph_tool.all" appears again and again. > > > > Any help? > > The directory "/usr/local/lib/python2.7/site-packages/" is probably not > in your python path. > > Try something like: > > export PYTHONPATH="/usr/local/lib/python2.7/site-packages/" > > Before running your python script. > > Cheers, > Tiago > > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > > > >

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graph-tool July 2012