October 2014 - 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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apt-get fail to download index files
by Andy Maloney 10 Mar '17

10 Mar '17

I am trying to install graph-tool on a Trusty Ubuntu virtualbox being hosted on a Mac. I've added the requisite lines deb http://downloads.skewed.de/apt/trusty trusty main deb-src http://downloads.skewed.de/apt/trusty trusty main to my /etc/apt/sources.list, but when I run a sudo apt-get update, I get the following errors: W: Failed to fetch http://downloads.skewed.de/apt/trusty/dists/trusty/Release Unable to find expected entry 'main/source/Sources' in Release file (Wrong sources.list entry or malformed file) E: Some index files failed to download. They have been ignored, or old ones used instead. I have the main, universe, and multiverse repositories available. If any one has come across this problem before, please let me know how to fix it. Thanks. Andy_

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Building graph-tool on CentOS 7
by Smith, Steven - 1004 - MITLL 28 Oct '16

28 Oct '16

The graph-tool make command on CentOS 7 fails at this point: $ cd graph-tool-2.2.35 $ ./configure --with-sparsehash-prefix=google $ make make all-recursive make[1]: Entering directory `/home/user/Downloads/graph-tool-2.2.35' Making all in src … make[4]: Entering directory `/home/user/Downloads/graph-tool-2.2.35/src/graph/topology' CXX graph_subgraph_isomorphism.lo graph_subgraph_isomorphism.cc: In instantiation of 'void get_subgraphs::operator()(const Graph1&, const Graph2*, VertexLabel, boost::any, EdgeLabel, boost::any, std::vector<VertexMap>&, size_t, bool, bool) const [with Graph1 = boost::adj_list<long unsigned int>; Graph2 = boost::adj_list<long unsigned int>; VertexLabel = boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >; EdgeLabel = boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >; VertexMap = boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >; size_t = long unsigned int]': /usr/include/c++/4.8.2/functional:1305:50: required from '_Result std::_Bind<_Functor(_Bound_args ...)>::__call_c(std::tuple<_Args2 ...>&&, std::_Index_tuple<_Indexes ...>) const [with _Result = void; _Args = {boost::adj_list<long unsigned int>&, boost::adj_list<long unsigned int>*&, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >&, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >&}; long unsigned int ..._Indexes = {0ul, 1ul, 2ul, 3ul, 4ul, 5ul, 6ul, 7ul, 8ul, 9ul}; _Functor = get_subgraphs; _Bound_args = {std::_Placeholder<1>, std::_Placeholder<2>, std::_Placeholder<3>, boost::any, std::_Placeholder<4>, boost::any, std::reference_wrapper<std::vector<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >, std::allocator<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> > > > >, long unsigned int, bool, bool}]’ … _descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_:: na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_:: na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope vertices_equivalent(make_property_map_equivalent(vertex_label1, vertex_label2))); ^ … , graph_tool::ConstantPropertyMap<bool, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope Any help fixing this would be greatly appreciated. I’m building graph-tool from the latest source, graph-tool-2.2.35.tar.bz2. CGAL is built successfully from source (there aren’t any cgal-devel packages yet in the .el7 repos), and because the .el 7 sparsehash-devel package puts its libraries in /usr/include/google, the specific ./configure command for CentOS 7 above is necessary. This runs successfully, and every compile up to graph_subgraph_isomorphism is successful.

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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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Simple Cycle Finder
by tanzairatier 25 Mar '16

25 Mar '16

Hello all, I'm wondering if anyone can suggest a strategy for finding elementary cycles with Graph-Tool. I'm working also with Network X, and they have a function for this, called simple_cycles(G). That function essentially runs Tarjan's Algorithm to find all strongly connected components, and then detects cycles within each of those components (this approach is called Johnson's Algorithm). I've tried to port the Network X code to Graph-Tool, but there are un-matching parallels in the data structures of both tools. e.g. Graph-Tool prefers to label with property maps. Since I've only begun using Graph-Tool a short while ago, this task is difficult for me. Any help would be appreciated, many thanks in advance. -- 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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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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Help regarding -enable-openMP
by Shubham Bhushan 11 Nov '15

11 Nov '15

Hi I asked earlier as to how utilize the parallel processing in my code. Now I installed it using the precompiled packages for Ubuntu. does that mean I'll have to reinstall it from source using the openmp option in the configure command? Shubham -- http://about.me/shubham.bhushan

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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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Fixing position of root vertex
by luistavares 25 Nov '14

25 Nov '14

Hi, I'm using the code below to fix the position of a root vertex. I'm developing an application and I wanna make sure that the root vertex is always located in the same place. g = Graph() v_pin = g.new_vertex_property("bool") v = g.add_vertex() v_pin[v] = True #root vertex ... pos = sfdp_layout(g, pin=v_pin) graph_draw(g, ...) I suppose it's working, but how I can confirm which one is the root vertex in my result? <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- 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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