graph-tool July 2013

graph-tool@skewed.de

11 participants
17 discussions

Problems With Graph tool install
by hirdt.john＠gmail.com 22 Jul '13

22 Jul '13

HI, I was a user of Networkx but my graphs have surpassed its capabilities. I am running Ubuntu 13.04 and I am trying to install graph-tool. I have the proper versions of GCC, Boost, Python, expat, scipy, numpy, CGAL, sparsehash, cairomn, pycairo, matplotlib and graphviz. I should be able to run on the command line sudo apt-get install python-graph-tool or sudo apt-get install graph-tool Neither work and are throwing the error E: Unable to locate package python-graph-tool and E: Unable to locate package graph-tool So I tried downloading the tar ball and extracting and running ./configure and that through the error ... configure: error: Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them. ============================================================================ I know that the Python library should not be the issue as I typed in the path and to no avail. If anyone sees anything obvious that I am missing or not doing please respond. Every other program I have ever wanted to install has been as easy as sudo apt-get install programname Thanks John

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Binary and compiled version living together
by Giuseppe Profiti 22 Jul '13

22 Jul '13

Hello, I would like to start extending graph-tools, but I wonder if it is possible to have the official release (installed from the repository) along with a custom compiled version. I don't know how python manages the libraries, so I'm wondering if it is possible to either: - switch from one library to the other when running the python script (like changing the classpath when running a java program) - change the library name, so I could do something like "import graph_tool" to get the official version and "import graph_tool_mydevel" to get my modified version If it is there any other (maybe easier) solution, please let me know. Thanks, Giuseppe

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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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Build assertion error
by Michael Tsikerdekis 19 Jul '13

19 Jul '13

Hi everyone, I am having trouble building from source on Ubuntu 10.04. I have 8GB of RAM. Before this error I was getting an error about boost/irange.h not found. I downloaded the latest version of boost and placed that directory on graph-tool to fix this. Seemed to correct other errors but now I am getting the following: user@wuwcorp:~/graph-tool-2.2.24$ make make all-recursive make[1]: Entering directory `/home/user/graph-tool-2.2.24' Making all in src make[2]: Entering directory `/home/user/graph-tool-2.2.24/src' Making all in graph make[3]: Entering directory `/home/user/graph-tool-2.2.24/src/graph' Making all in centrality make[4]: Entering directory `/home/user/graph-tool-2.2.24/src/graph/centrality' CXX graph_pagerank.lo cc1plus: malloc.c:3551: munmap_chunk: Assertion `ret == 0' failed. In file included from ./../graph_filtering.hh:55, from graph_pagerank.cc:18: ./../mpl_nested_loop.hh: In member function 'void boost::mpl::nested_for_each<TR1, TR2, TR3, TR4, TR5>::eval_action4<Action, T1, T2, T3>::operator()(T4) const [with T4 = boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<long unsigned int> >, Action = boost::mpl::selected_types<graph_tool::detail::action_wrap<boost::_bi::bind_t<void, graph_tool::get_pagerank, boost::_bi::list9<boost::arg<1>, boost::_bi::value<boost::typed_identity_property_map<long unsigned int> >, boost::arg<2>, boost::arg<3>, boost::arg<4>, boost::_bi::value<double>, boost::_bi::value<double>, boost::_bi::value<long unsigned int>, boost::reference_wrapper<long unsigned int> > >, mpl_::bool_<false> > >, T1 = boost::reverse_graph<boost::filtered_graph<boost::adj_list<long unsigned int>, boost::keep_all, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<long unsigned int> > > >, const boost::filtered_graph<boost::adj_list<long unsigned int>, boost::keep_all, graph_tool::detail::MaskFilter<boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<long unsigned int> > > >&>*, T2 = boost::checked_vector_property_map<long double, boost::typed_identity_property_map<long unsigned int> >, T3 = boost::checked_vector_property_map<long int, boost::typed_identity_property_map<long unsigned int> >, TR1 = graph_tool::detail::graph_action<boost::_bi::bind_t<void, graph_tool::get_pagerank, boost::_bi::list9<boost::arg<1>, boost::_bi::value<boost::typed_identity_property_map<long unsigned int> >, boost::arg<2>, boost::arg<3>, boost::arg<4>, boost::_bi::value<double>, boost::_bi::value<double>, boost::_bi::value<long unsigned int>, boost::reference_wrapper<long unsigned int> > >, graph_tool::detail::all_graph_views, mpl_::bool_<false>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, boost::mpl::v_item<graph_tool::ConstantPropertyMap<double, long unsigned int>, boost::mpl::v_item<boost::typed_identity_property_map<long unsigned int>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<long int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<short int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, boost::mpl::v_item<graph_tool::ConstantPropertyMap<double, std::tr1::tuple<long unsigned int, long unsigned int, long unsigned int> >, boost::mpl::v_item<boost::adj_edge_index_property_map<long unsigned int>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<long int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<short int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, boost::mpl::vector<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, mpl_::na, mpl_::na> >::graph_view_pointers, TR2 = boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, TR3 = boost::mpl::v_item<graph_tool::ConstantPropertyMap<double, long unsigned int>, boost::mpl::v_item<boost::typed_identity_property_map<long unsigned int>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<long int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<short int, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::typed_identity_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, TR4 = boost::mpl::v_item<graph_tool::ConstantPropertyMap<double, std::tr1::tuple<long unsigned int, long unsigned int, long unsigned int> >, boost::mpl::v_item<boost::adj_edge_index_property_map<long unsigned int>, boost::mpl::v_item<boost::checked_vector_property_map<long double, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<double, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<long int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<short int, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::v_item<boost::checked_vector_property_map<unsigned char, boost::adj_edge_index_property_map<long unsigned int> >, boost::mpl::vector0<mpl_::na>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, 0>, TR5 = boost::mpl::vector<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, mpl_::na, mpl_::na>]': ./../mpl_nested_loop.hh:186: internal compiler error: Aborted Please submit a full bug report, with preprocessed source if appropriate. See <file:///usr/share/doc/gcc-4.4/README.Bugs> for instructions. make[4]: *** [graph_pagerank.lo] Error 1 make[4]: Leaving directory `/home/user/graph-tool-2.2.24/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/user/graph-tool-2.2.24/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/graph-tool-2.2.24/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/graph-tool-2.2.24' make: *** [all] Error 2 Best, Michael Tsikerdekis

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Tool tips / interactive drawing output
by John Reid 12 Jul '13

12 Jul '13

Hi, First of all, thanks for a great library with great documentation. I'm just starting with graph-tool but so far it looks really nice. I have previously used the now unmaintained BGL-python bindings and for me it is good that graph-tool seems to have some similarities in its API. My question is: I often have large graphs where I cannot display vertex labels in the output for reasons of space. I would really love to draw these graphs to a format where I could hover with the mouse to produce tool tips to show vertex labels, etc... Is this possible? Thanks, John.

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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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isolate layout functions from gt.draw?
by Richard Ree 10 Jul '13

10 Jul '13

I'm trying to use the node positions calculated by sfdp_layout in a galry visualization, but am running into the problem of conflicting GTK+ symbols (galry uses GTK+ 2). I'm thinking this could be avoided if the layout functions were not part of gt.draw... but any suggestions for a workaround? Thanks, -Rick

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graph-tool July 2013