March 2016 - graph-tool - archives.skewed.de

find community classes/labels
by yinjunjun 04 Jul '16

04 Jul '16

Hi, I am trying to use graph tool to extract communities, and I used the minimize_blockmodel_dl function. However, after it has been executed successfully, I wish to know each vertex and information of which community it belongs to, and I can not figure out how. For example, state = graph_tool.community.minimize_blockmodel_dl(g, parallel=True) ##print state.b print state.get_blocks().get_array() it give me an array of all the vertex in zero. Could any one point me to the right directions. Thank you very much. Best Regards Junjun -- 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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OS X Macports clang with openmp build of graph-tool
by Steve 05 Apr '16

05 Apr '16

Macports clang 3.7 and 3.8 now support openmp, which creates the opportunity to build graph-tool on OS X with OpenMP speeds.I've tried the following, which haven't quite worked yet, but it's close. Any pointers would be appreciated. sudo port uninstall py-graph-tool py27-graph-tool sudo port clean --dist py-graph-tool py27-graph-tool sudo port install clang-3.8 +openmp sudo port -d install py-graph-tool py27-graph-tool configure.compiler=macports-clang-3.8 configure.args=--enable-openmp I expected the option "configure.args=--enable-openmp" would tell the autoconf'd ./configure command to specify --enable-openmp, but it does not: DEBUG: Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-graph-tool/py27-graph-tool/work/graph-tool-2.13" && ./configure --prefix=/opt/local --with-boost=/opt/local --exec-prefix=/opt/local/Library/Frameworks/Python.framework/Versions/2.7 … checking whether to enable parallel algorithms with openmp... no The port notes for clang-3.8 say: Use with clang-3.[78] (when built with +openmp variant) by adding "-fopenmp" to your compile and link lines. (Or "-I/opt/local/include/libomp -L/opt/local/lib/libomp -fopenmp" if clang is installed without +openmp.) Based on the Port Phases <https://guide.macports.org/chunked/reference.phases.htm> page, I've tried a variety of options like configure.cxxflags-append=-fopenmp, all without success. Perhaps a custom portfile is necessary, but this would be easiest to address through the port command line. -- 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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Accounting for vertex size when setting the layout
by Andrew 30 Mar '16

30 Mar '16

I just started playing around with graphtool. I can create and draw a twitter graph fairly easily. However, I would like the size of each vertex to be a function of the vertex's degree. I can map the size of each vertex, but then when I use the sfdp layout, there is significant overlap. What is the best way around this? -- 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 the output positions in sfdp layout
by Kimon 29 Mar '16

29 Mar '16

Hi I am trying to fix the layout that I get every time that I re-run my script. I gave input pos to sfdp a propertymap that initializes all positions to [1,1]. However, the output pos that I am getting is slightly different every time. Any solutions? 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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Dice or Jaccard similarity of vertices
by Alexey Strokach 27 Mar '16

27 Mar '16

Hi, Is there a method to calculate the Dice or the Jaccard similarity between *all pairs of vertices* in the graph? Similar to the similarity_dice <http://igraph.org/python/doc/igraph.GraphBase-class.html#similarity_dice> and similarity_jaccard <http://igraph.org/python/doc/igraph.GraphBase-class.html#similarity_jaccard> methods in igraph? I searched through graph_tool documentation, and google, but did not find anything. Thanks, Alexey

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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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Edges of plot as a vertex
by Ito 23 Mar '16

23 Mar '16

Greetings I'd like to plot a graph where the edges around the plot represent a specific vertex. Lacking a better example think of it as a spherical panoramic photography where the edges of the picture are a single point. Might that that be possible with graph-tool (any graph tool)? Thanks! Ito

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Segmentation fault when I try to access to a vertex
by Eric 22 Mar '16

22 Mar '16

Hi, I have a segmentation fault create with a specific data set (other data set works). I have some difficulty to find the origin. I try to create a small example, but for the moment I can only give you the output and backtrack of gdb: *Output:* Program received signal SIGSEGV, Segmentation fault. 0x00007ffff0473d62 in uw_init_context_1 () from /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 Missing separate debuginfos, use: debuginfo-install atlas-3.8.4-2.el6.x86_64 boost-iostreams-1.41.0-27.el6.x86_64 boost-python-1.41.0-27.el6.x86_64 boost-regex-1.41.0-27.el6.x86_64 boost-system-1.41.0-27.el6.x86_64 boost-thread-1.41.0-27.el6.x86_64 bzip2-libs-1.0.5-7.el6_0.x86_64 fontconfig-2.8.0-5.el6.x86_64 freetype-2.3.11-15.el6_6.1.x86_64 glibc-2.12-1.166.el6.x86_64 keyutils-libs-1.4-5.el6.x86_64 krb5-libs-1.10.3-42.el6.x86_64 libX11-1.6.0-6.el6.x86_64 libXau-1.0.6-4.el6.x86_64 libXext-1.3.2-2.1.el6.x86_64 libXrender-0.9.8-2.1.el6.x86_64 libcom_err-1.41.12-22.el6.x86_64 libicu-4.2.1-12.el6.x86_64 libjpeg-turbo-1.2.1-3.el6_5.x86_64 libpng-1.2.49-2.el6_7.x86_64 libselinux-2.0.94-5.8.el6.x86_64 libtiff-3.9.4-10.el6_5.x86_64 libxcb-1.9.1-3.el6.x86_64 openssl-1.0.1e-42.el6_7.2.x86_64 pango-1.28.1-10.el6.x86_64 python-libs-2.6.6-64.el6.x86_64 sqlite-3.6.20-1.el6_7.2.x86_64 zlib-1.2.3-29.el6.x86_64 *bt*: #0 0x00007ffff0473d62 in uw_init_context_1 () from /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 #1 0x00007ffff047420e in _Unwind_RaiseException () from /soft/bioinfo/linux_RH6/gcc-4.9.3/lib64/libgcc_s.so.1 #2 0x00007ffff06d833b in __cxa_throw () at ../../../../libstdc++-v3/libsupc++/eh_throw.cc:82 #3 0x00007fffe4ae40f3 in _ZNK10graph_tool6detail12graph_actionISt5_BindIFNS_14add_new_vertexESt12_PlaceholderILi1EESt17reference_wrapperINS_14GraphInterfaceEEmS6_IN5boost6python3api6objectEEEENS0_15all_graph_viewsEN4mpl_5bool_ILb0EEEJEEclIJEEEvDpOT_ () from /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #4 0x00007fffe4a51dee in graph_tool::add_vertex(graph_tool::GraphInterface&, unsigned long) () from /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #5 0x00007fffe4a92bfe in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::api::object (*)(graph_tool::GraphInterface&, unsigned long), boost::python::default_call_policies, boost::mpl::vector3<boost::python::api::object, graph_tool::GraphInterface&, unsigned long> > >::operator()(_object*, _object*) () from /***********/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #6 0x00007fffe303ca86 in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib64/libboost_python.so.5 #7 0x00007fffe303cd98 in ?? () from /usr/lib64/libboost_python.so.5 #8 0x00007fffe30452a3 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const () from /usr/lib64/libboost_python.so.5 #9 0x00007fffe3ea37a3 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<graph_tool::ValueException, void (*)(graph_tool::ValueException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(graph_tool::ValueException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /********/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #10 0x00007fffe304527d in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const () from /usr/lib64/libboost_python.so.5 #11 0x00007fffe3ea36d3 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<graph_tool::IOException, void (*)(graph_tool::IOException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(graph_tool::IOException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #12 0x00007fffe304527d in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const () from /usr/lib64/libboost_python.so.5 #13 0x00007fffe3ea3603 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<graph_tool::GraphException, void (*)(graph_tool::GraphException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(graph_tool::GraphException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /*******/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so #14 0x00007fffe3045063 in boost::python::handle_exception_impl(boost::function0<void>) () from /usr/lib64/libboost_python.so.5 #15 0x00007fffe303a928 in ?? () from /usr/lib64/libboost_python.so.5 #16 0x00000000004197c7 in PyObject_Call (func=0x1c0f070, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #17 0x00000000004a80b0 in do_call (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4239 #18 call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4044 #19 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2666 #20 0x00000000004aa627 in PyEval_EvalCodeEx (co=0x10b66b0, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=1, kws=0x44c8a56c8, kwcount=0, defs=0x1bf7b28, defcount=1, closure=0x0) at Python/ceval.c:3253 #21 0x00000000004a87d4 in fast_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4117 #22 call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4042 #23 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2666 . . (loop) . #124095 0x00000000004a9ab5 in fast_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4107 #124096 call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4042 #124097 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2666 #124098 0x00000000004aa627 in PyEval_EvalCodeEx (co=0x7ffff7ece530, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3253 #124099 0x00000000004aa732 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:667 ---Type <return> to continue, or q <return> to quit--- #124100 0x00000000004cad5e in run_mod (fp=0x8f3600, filename=0x7fffffffdc71 "/*****/nektar_graph.py", start=<value optimized out>, globals=0x7fe690, locals=0x7fe690, closeit=1, flags=0x7fffffffd760) at Python/pythonrun.c:1370 #124101 PyRun_FileExFlags (fp=0x8f3600, filename=0x7fffffffdc71 "/*******/nektar_graph.py", start=<value optimized out>, globals=0x7fe690, locals=0x7fe690, closeit=1, flags=0x7fffffffd760) at Python/pythonrun.c:1356 #124102 0x00000000004caf87 in PyRun_SimpleFileExFlags (fp=0x8f3600, filename=0x7fffffffdc71 "/*********/nektar_graph.py", closeit=1, flags=0x7fffffffd760) at Python/pythonrun.c:948 #124103 0x0000000000414e72 in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:640 #124104 0x000000339ee1ed5d in __libc_start_main () from /lib64/libc.so.6 I use the last version of graph-tool(2.12), with python-2.7.6, gcc-4.9.3, boost-1.59.0. Should I try with python-3.X ? It will be useful, if you have any advice or information to found the origin of this segmentation fault. Without I comeback when I have more information. Regards, Eric. -- 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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Export edge list to ndarray (numpy)
by Josh Levy-Kramer 22 Mar '16

22 Mar '16

Hi, I would like to create a function which quickly exports a Graph to an edge list in Python. Bassically the opposite to the `Graph.add_edge_list` method. My current solution is: edge_list = [ [int(e.source()), int(e.target())] for e in g.edges()] As you can imagine this is very slow as the iteration is done in Python and not C++. Has anyone done this before, or knows how to do this at C++ speed? Many thanks, Josh Levy-Kramer Data Scientist @ Starcount

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