June 2013 - graph-tool - archives.skewed.de

What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- 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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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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graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> 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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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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Re: [graph-tool] Compilation error with Weave inline
by Giovanni Luca Ciampaglia 19 Jul '13

19 Jul '13

Hi Tiago, thanks for you reply: On 06/28/2013 08:00 AM, graph-tool-request(a)skewed.de wrote: > > The code you're trying to run is not valid C++ (you cannot mix typedefs > and variable definitions). Furthermore you should not try to guess the > type of the graph, and instead you should use the pre-defined > typedefs. I see. Time to grab a copy of intro to C++ then ;-) > You have to use the following code: > > _add_code = ''' > using namespace boost; > > typedef graph_traits<graph_graph_t>::vertex_descriptor vertex_t; > > for (int i = 0; i < n; ++i) > { > add_edge(vertex_t(edges[i, 0]), vertex_t(edges[i, 1]), graph); > } > ''' > > Modifying your script with the above code worked for me. Note that you > have to use the development version of graph-tool in git, since the > current version has a bug in the run_action module. I cloned the repository, ran autogen.sh, but it doesn't produce any configure script (attached the console output). Am I missing some step? > > I think that a function to add several edges at once is a useful one. If > you open a ticket for it, I'll implement it when I find some time. Sure! >> Alternatively, how do I get to call BGL's add_edge with the wrapped >> graph type, i.e. the one typedef'd automatically by inline? > Everything should work fine with the properly overloaded > functions... I.e., whenever you call add_edge(), it should select the > appropriately overloaded function for the correct type. > > Cheers, > Tiago -- Giovanni Luca Ciampaglia Postdoctoral fellow Center for Complex Networks and Systems Research Indiana University ✎ 910 E 10th St ∙ Bloomington ∙ IN 47408 ☞ http://cnets.indiana.edu/ ✉ gciampag(a)indiana.edu

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Building on OSX 10.8 with brew, Anaconda Python distribution
by Eric Jonas 10 Jul '13

10 Jul '13

Hey guys! I'm trying to build graph-tool and I'm using: OSX 10.8 brew The latest Anaconda python distribution from Continuum. When building the blockmodel I'm getting the following error: graph_blockmodel.hh:910: error: no matching function for call to 'get(const boost::tuples::tuple<boost::UndirectedAdaptor<boost::filtered_graph<boost::adj_list<long unsigned int>, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::adj_edge_index_property_map<long unsigned int> > >, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<long unsigned int> > > > >::EdgeDescriptor, bool, long unsigned int, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>&)' The (now complex) configure command I'm using is: LDFLAGS=-L/usr/local/opt/boost149/lib CPPFLAGS="-I/usr/local/opt/boost149/include -I/usr/local/include/sparsehash" CC=gcc-4.7 PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig/ ./configure --prefix=`python2.7-config --prefix` which ultimately gives the output in the gist at : https://gist.github.com/ericmjonas/5613858 I've tried explicitly using boost 1.49 and boost 1.52, as well as GCC-4.7 (and clang) and still always get this error. I'm sort of out of next steps -- any pointers? ...Eric

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Compilation error with Weave inline
by Giovanni Luca Ciampaglia 27 Jun '13

27 Jun '13

Hi, I recently moved from NetworkX to graph-tool and I am very impressed with the performance increase, good job! A bit for learning and also for speeding up a code that creates a graph dynamically, I am trying to implement a batch insertion function with Weave, but I am running into a compilation error. My knowledge of C++ is sketchy at best so please forgive if I am asking something really dumb -- though I suspect that the problem is more in the way graph_tool interacts with the BGL. Anyway, the code is here: https://gist.github.com/junkieDolphin/5868934 The error I get is: > /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:822:13: > error: ‘adjacency_list’ does not name a type (full trace below) So I suspect the problem is in how I tell run_inline to include the proper header files in the generated source. Putting them before the loop is clearly not an option, because it would put the #includes in the middle of a scope. Any idea? Alternatively, how do I get to call BGL's add_edge with the wrapped graph type, i.e. the one typedef'd automatically by inline? Thanks! Giovanni >> In [33]: %run graph_utils.py >> Python mode >> Python mode added 100 edges in 0.0191810131073 seconds >> Weave mode >> In file included from >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0, >> from >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, >> from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:15, >> from >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:22: >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: >> warning: #warning "Using deprecated NumPy API, disable it by #defining >> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp: >> In function ‘PyObject* compiled_func(PyObject*, PyObject*)’: >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:822:13: >> error: ‘adjacency_list’ does not name a type >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:27: >> warning: left operand of comma operator has no effect [-Wunused-value] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:40: >> warning: left operand of comma operator has no effect [-Wunused-value] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:44: >> error: ‘_graph’ was not declared in this scope >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:747:15: >> warning: unused variable ‘Nedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:748:15: >> warning: unused variable ‘Sedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:749:9: >> warning: unused variable ‘Dedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp: >> At global scope: >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:713:18: >> warning: unused parameter ‘self’ [-Wunused-parameter] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_doc’ >> [-Wmissing-field-initializers] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_flags’ >> [-Wmissing-field-initializers] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_doc’ >> [-Wmissing-field-initializers] >> In file included from >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0, >> from >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, >> from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:15, >> from >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:22: >> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: >> warning: #warning "Using deprecated NumPy API, disable it by #defining >> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp: >> In function ‘PyObject* compiled_func(PyObject*, PyObject*)’: >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:822:13: >> error: ‘adjacency_list’ does not name a type >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:27: >> warning: left operand of comma operator has no effect [-Wunused-value] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:40: >> warning: left operand of comma operator has no effect [-Wunused-value] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:826:44: >> error: ‘_graph’ was not declared in this scope >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:747:15: >> warning: unused variable ‘Nedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:748:15: >> warning: unused variable ‘Sedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:749:9: >> warning: unused variable ‘Dedges’ [-Wunused-variable] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp: >> At global scope: >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:713:18: >> warning: unused parameter ‘self’ [-Wunused-parameter] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_doc’ >> [-Wmissing-field-initializers] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_flags’ >> [-Wmissing-field-initializers] >> /home/giovanni/.python27_compiled/sc_d9500bfc215fd29698821c3db4d6aeb81.cpp:885:1: >> warning: missing initializer for member ‘PyMethodDef::ml_doc’ >> [-Wmissing-field-initializers] > > -- Giovanni Luca Ciampaglia Postdoctoral fellow Center for Complex Networks and Systems Research Indiana University ✎ 910 E 10th St ∙ Bloomington ∙ IN 47408 ☞ http://cnets.indiana.edu/ ✉ gciampag(a)indiana.edu

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