graph-tool July 2014

graph-tool@skewed.de

16 participants
27 discussions

How BIG is your graph
by Helen Lampesis 14 Jul '14

14 Jul '14

Dear graphErs, I am about to start a project working on a graph with about 50M Nodes and 1B edges and I want your opinion regarding the feasibility of this endeavor with graph_tool. Can you please share your experience with graph examples that were comparable in size? I mostly want to calculate centrality measures and I will need to apply (several) filters to isolate nodes with particular attributes. On top of it, I am running on a super-computer (so memory is NOT an issue) and if I am lucky they have installed/enabled the parallel version of the library. Thank you very much, He

3 2

How vertex and edge properties are taken into account in clustering.motifs
by sabrina 14 Jul '14

14 Jul '14

Hello, Please, I would like to know if vertex and edge properties of a graph are taken into account in clustering.motifs. In my graph, edge properties are some int labels with two possible values (as shown in the image <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> ). When I use clustering motifs, it returns 1 motif with 2 nodes and this motif occurs 5 times in the original graph. In [144]: motifs, counts, vm = gt.motifs(grafo, 2, return_maps=True) In [145]: motifs Out[145]: [<Graph object, undirected, with 2 vertices and 1 edge at 0xba12c6c>] In [146]: counts Out[146]: [5] In [148]: len(vm) Out[148]: 1 In [149]: len(vm[0]) Out[149]: 5 It seems to me that clustering.motifs does not take into account vertex and edge properties. Is it true? Is there any way to generate motifs that take into account the vertex and edge properties? In my example, I expected that there would be 2 motifs Motif 1: 2 nodes and 1 edge with label 10, which occurs 2 times in the original graph. Motif 2: 2 nodes and 1 edge with label 13, which occurs 3 times in the original graph. Thank you for any help you can provide, Sabrina -- 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.

2 1

numbers format
by Flavien Lambert 08 Jul '14

08 Jul '14

Hi guys, when saving a graph with .save(), I understood that float are represented in hexadecimal exponentiation format. I was wondering the reason for that. The thing behind my question is that I built a graph with 5M vertices and 50M edges so storing it as an XML file leads to a 5GB one. So, if I can find a way to reduce the size, I will be very happy. Best, F.

3 3

Extracting vertices with a given property
by Flavien Lambert 08 Jul '14

08 Jul '14

Hi all, I was wondering if there is a clever way to extract the list of vertices with a given value of a property or if you have to run a loop on the vertices on build the list by hand (I searched on the documentation but did not find it...). Thanks, F.

4 7

Gtk-WARNING
by Simons, Gareth 06 Jul '14

06 Jul '14

I am getting the following warning when using graph_draw: (process:23214): Gtk-WARNING **: Locale not supported by C library. Using the fallback 'C' locale. Dynamic session lookup supported but failed: launchd did not provide a socket path, verify that org.freedesktop.dbus-session.plist is loaded! Fontconfig warning: ignoring UTF-8: not a valid region tag It appears that the output file is still successfully rendered to .png. I am not sure what the implications of the warning are, how to remedy, or what, if anything, is affected by it? Thanks.

4 17

Gtk error : matplotlib graphtool interaction
by jean-patrick 03 Jul '14

03 Jul '14

Hello, It seems that maplotlib and graph_tool can't live in the same python file. When the following code is run from an ide (spyder or ninja) an error is produced: import matplotlib.pyplot as plt import graph_tool.all as gt import numpy as np x = np.arange(0,7,0.1) y =np.sin(x) plt.plot(x,y) yield the error: (test-graphtool-matplotlib.py:5555): Gtk-ERROR **: GTK+ 2.x symbols detected. Using GTK+ 2.x and GTK+ 3 in the same process is not supported Matplotlib was build with ubuntu 14.04: >>> print matplotlib.__version__ 1.3.1 and graph_tool was installed from a deb. When a similar code is run from an ipython notebook, there's no error! test-matplotlib-graph_tool.ipynb <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> jean-patrick -- 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.

2 4

OS X make file errors
by Ted Fujimoto 03 Jul '14

03 Jul '14

I'm trying to install graph-tool from source since I rely on Anaconda. I'm getting the following errors (using OS X 10.9 with Boost version 1.55.0_2): teds-mbp:graph-tool tf$ make (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/tf/Desktop/GitStuff/graph-tool/missing autoheader) configure.ac:34: warning: AC_ARG_PROGRAM was called before AC_CANONICAL_TARGET ../../lib/autoconf/general.m4:1854: AC_CANONICAL_TARGET is expanded from... configure.ac:34: the top level configure.ac:214: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:197: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2598: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2608: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from... ../../lib/autoconf/general.m4:2046: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2059: AC_CACHE_CHECK is expanded from... m4/ax_boost_python.m4:99: AX_BOOST_PYTHON is expanded from... configure.ac:214: the top level configure.ac:218: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:197: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2598: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2608: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from... ../../lib/autoconf/general.m4:2046: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2059: AC_CACHE_CHECK is expanded from... m4/ax_boost_iostreams.m4:89: AX_BOOST_IOSTREAMS is expanded from... configure.ac:218: the top level configure.ac:222: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:197: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2598: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2608: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from... ../../lib/autoconf/general.m4:2046: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2059: AC_CACHE_CHECK is expanded from... m4/ax_boost_regex.m4:84: AX_BOOST_REGEX is expanded from... configure.ac:222: the top level configure.ac:227: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:197: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2598: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2608: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from... ../../lib/autoconf/general.m4:2046: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2059: AC_CACHE_CHECK is expanded from... m4/ax_boost_graph.m4:90: AX_BOOST_GRAPH is expanded from... configure.ac:227: the top level rm -f stamp-h1 touch config.h.in cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in src Making all in graph Making all in centrality CXX graph_betweenness.lo warning: unknown warning option '-Wno-unused-local-typedefs' [-Wunknown-warning-option] In file included from graph_betweenness.cc:18: In file included from ./../graph_filtering.hh:21: ./../graph.hh:167:5: error: too many template parameters in template redeclaration template <class Action, class GraphViews, class Wrap, class TR1, class TR2, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./../graph.hh:50:1: note: previous template declaration is here template <class Action, class GraphViews, class Wrap = boost::mpl::false_, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from graph_betweenness.cc:18: In file included from ./../graph_filtering.hh:55: ./../mpl_nested_loop.hh:91:40: error: use 'template' keyword to treat 'join' as a dependent template name nested_for_each_imp<TRS...>(_a.join<T>()); ^ template In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:482:27: error: '_mg' is a private member of 'graph_tool::GraphInterface' max(g._mg->get_last_index(), size_t(1))) {} ^ ./../graph_filtering.hh:512:16: note: in instantiation of member function 'graph_tool::detail::graph_action<std::__1::__bind<get_weighted_betweenness, std::__1::placeholders::__ph<1> &, boost::typed_identity_property_map<unsigned long>, std::__1::placeholders::__ph<2> &, std::__1::placeholders::__ph<3> &, boost::any &, bool &, unsigned long, unsigned long>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0> >::graph_action' requested here return detail::graph_action<Action,GraphViews,Wrap,TRS...>(g, st... ^ graph_betweenness.cc:142:13: note: in instantiation of function template specialization 'graph_tool::run_action<graph_tool::detail::all_graph_views, mpl_::bool_<false> >::operator()<std::__1::__bind<get_weighted_betweenness, std::__1::placeholders::__ph<1> &, boost::typed_identity_property_map<unsigned long>, std::__1::placeholders::__ph<2> &, std::__1::placeholders::__ph<3> &, boost::any &, bool &, unsigned long, unsigned long>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0> >' requested here (g, std::bind<>(get_weighted_betweenness(), ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:481:43: error: '_mg' is a private member of 'graph_tool::GraphInterface' : _g(g), _a(a, g, num_vertices(*g._mg), ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:482:27: error: '_mg' is a private member of 'graph_tool::GraphInterface' max(g._mg->get_last_index(), size_t(1))) {} ^ ./../graph_filtering.hh:512:16: note: in instantiation of member function 'graph_tool::detail::graph_action<std::__1::__bind_r<void, get_betweenness, std::__1::placeholders::__ph<1> &, boost::typed_identity_property_map<unsigned long>, std::__1::placeholders::__ph<2> &, std::__1::placeholders::__ph<3> &, bool &, unsigned long>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0> >::graph_action' requested here return detail::graph_action<Action,GraphViews,Wrap,TRS...>(g, st... ^ graph_betweenness.cc:154:13: note: in instantiation of function template specialization 'graph_tool::run_action<graph_tool::detail::all_graph_views, mpl_::bool_<false> >::operator()<std::__1::__bind_r<void, get_betweenness, std::__1::placeholders::__ph<1> &, boost::typed_identity_property_map<unsigned long>, std::__1::placeholders::__ph<2> &, std::__1::placeholders::__ph<3> &, bool &, unsigned long>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0> >' requested here (g, std::bind<void>(get_betweenness(), std::placeholders::_1, ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:481:43: error: '_mg' is a private member of 'graph_tool::GraphInterface' : _g(g), _a(a, g, num_vertices(*g._mg), ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:482:27: error: '_mg' is a private member of 'graph_tool::GraphInterface' max(g._mg->get_last_index(), size_t(1))) {} ^ ./../graph_filtering.hh:512:16: note: in instantiation of member function 'graph_tool::detail::graph_action<std::__1::__bind<get_central_point_dominance, std::__1::placeholders::__ph<1> &, std::__1::placeholders::__ph<2> &, std::__1::reference_wrapper<double> >, graph_tool::detail::never_reversed, mpl_::bool_<false>, boost::mpl::v_item<boost::typed_identity_property_map<unsigned long>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<long long, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<short, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0> >::graph_action' requested here return detail::graph_action<Action,GraphViews,Wrap,TRS...>(g, st... ^ graph_betweenness.cc:179:9: note: in instantiation of function template specialization 'graph_tool::run_action<graph_tool::detail::never_reversed, mpl_::bool_<false> >::operator()<std::__1::__bind<get_central_point_dominance, std::__1::placeholders::__ph<1> &, std::__1::placeholders::__ph<2> &, std::__1::reference_wrapper<double> >, boost::mpl::v_item<boost::typed_identity_property_map<unsigned long>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<long long, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<short, boost::typed_identity_property_map<unsigned long> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0> >' requested here (g, std::bind<>(get_central_point_dominance(), std::placeholders::_1, ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ In file included from graph_betweenness.cc:18: ./../graph_filtering.hh:481:43: error: '_mg' is a private member of 'graph_tool::GraphInterface' : _g(g), _a(a, g, num_vertices(*g._mg), ^ ./../graph.hh:177:30: note: declared private here shared_ptr<multigraph_t> _mg; ^ 1 warning and 8 errors generated. make[4]: *** [graph_betweenness.lo] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2

3 2

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

graph-tool July 2014