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

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

3 5

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.

3 2

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.

3 7

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

5 9

Consistent colour scale and legend
by Alexandra Diem 17 Mar '16

17 Mar '16

Hi, I'm trying to use graph-tool to track concentrations on a network and was wondering what the best way would be to obtain consistent colour scales for a vertex property? I track the concentration of a substance as a vertex property and then use that as the vertex_fill_color in graph_draw because I would like to visualise the change in concentration over the network over time. This works great, but it appears that every time I plot the graph the colormap is rescaled to the minimum and maximum values in the vertex property. So if my values range from 0.0 to 0.4 and I use the Blues colormap 0.0 is white and 0.4 is dark blue. If in the next time step my values range from 0.0 to 0.6 then 0.6 is dark blue and 0.4 is now a different shade of blue. Instead, if I know 0.0 would be the minimum value and 1.0 would be the maximum I would like to consistently plot my graphs using that scaling, so that 0.4 always has the same shade of blue. I hope this all made sense. Thanks! Alexandra

4 5

Compiling Error
by gaolongnuaa 01 Mar '16

01 Mar '16

Hi Tiago, I'm very interested in using graph-tools to do network analysis since my network is pretty large. After I installed those required dependency packages, I still got errors when I run make. The error message is as following which I could not figure out. ./configure CPPFLAGS="-I/home/gaol3/Software/Tools/boost/include -I/home/gaol3/Software/Tools/CGAL/include" LDFLAGS="-L/home/gaol3/Software/Tools/boost/lib -L/home/gaol3/Software/Tools/CGAL/lib" --disable-sparsehash make make[4]: *** [graph_hits.lo] Error 1 make[4]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12' make: *** [all] Error 2 Thanks, Long -- 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

Segmentation fault when using minimize_blockmodel_dl for community detection
by hao 01 Mar '16

01 Mar '16

Hi Tiago: I got Segmentation fault when using minimize_blockmodel_dl to discover communities from a graph. The following is the output in the terminal: ------------------- *** Error in `*** Error in `python*** Error in `python': double free or corruption (out): 0x00007fe6a8000c30 *** *** Error in `python': double free or corruption (!prev): 0xpython': double free or corruption (!prev): 0x0000000051abe1a0 *** Segmentation fault ------------------- This happens when I specify the parameter parallel = True for the method minimize_blockmodel_dl. I am wondering whether this segmentation fault has something to do with the synchronization between threads when specifying the parallel = True parameter. The graph-tool I am using is 2.7 (commit ebd75c28, Thu Sep 17 23:25:50 2015 +0200). Is this fixed in the latest version? Thanks. Best Regards~ Hao -- 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.

3 7

About avg_neighbour_corr
by scuenda 22 Feb '16

22 Feb '16

Dear Tiago, Graph-tool is a great and ultra-fast library. It saved me tons of hours doing some statistics with heavy graphs. Thank you so much for your great work. However, right now I'm having some troubles with the function avg_neighbour_corr. I must missing something, but I don't know what it is. Imagine we consider a directed graph g, and its reverse graph h. Then, if we calculate goo = avg_neighbour_corr(g, "out", "out") hii = avg_neighbour_corr(h, "in", "in") I guessed both results should be the same, but they are not. It must be related to the results of the function corr_hist, which returns the transposed matrix of g for h. However, I fail to see why, considering that the in-degree vertex property of h is the same as the out-degree vertex property of g, and all edges are reversed in h. Any help, please? Thanks in advance. Best, Sara. PS: Here is the code of a dummy example for a network g given by: (2) <==> (0) ----> (1) ----> (2) #### code g = gt.Graph() g.add_edge_list([(0,1), (0,2), (1,2), (2,0)]) h = gt.GraphView(g, reversed = True) goo = avg_neighbour_corr(g, "out", "out") hii = avg_neighbour_corr(h, "in", "in") #### end of code #### results # >>> goo[0] # array([ nan, 1.5, 1. ]) # >>> hii[0] # array([ nan, 1.66666667, 1. ]) -- 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 2

import of graph_tool hangs (Ubuntu 15.10)
by Chris Barrington-Leigh 22 Feb '16

22 Feb '16

I have followed the instructions for Ubuntu here https://graph-tool.skewed.de/download#debian to install the precompiled version of graph-tool onto my Ubuntu 15.10 system. It went okay except that I got the complaint, even after installing the key, that the graph-tool package wasn't verified. After installation, there seems to be a conflict between graph_tool and pylab. I usually start python 2.7 under ipython with ipython --pdb --pylab After doing so, the following works alright from graph_tool import Graph However, the following hangs forever: from graph_tool.all import graph_draw /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: cannot register existing type 'GtkWidget' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: cannot add class private field to invalid type '<invalid>' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: cannot add private field to invalid (non-instantiatable) type '<invalid>' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: g_type_add_interface_static: assertion 'G_TYPE_IS_INSTANTIATABLE (instance_type)' failed g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: cannot register existing type 'GtkBuildable' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: g_type_interface_add_prerequisite: assertion 'G_TYPE_IS_INTERFACE (interface_type)' failed g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:176: Warning: g_once_init_leave: assertion 'result != 0' failed g_type = info.get_g_type() I don't understand the errors, but possibly some test could avert the hang/crash outcome? Thanks, Chris -- 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.

3 6

Local clustering coefficient normalization
by Danilo Giuffrida 08 Feb '16

08 Feb '16

Hi Tiago, I have extensively used graph-tool, and I find it very nice and efficient so, first of all, congratulations for your work. I write to you because of a suspected bug in the local clustering coefficient, which results normalized in [0, 2] instead than in [0,1] for one of my datasets. This issue is probably due to the fact that the network was obtained by "simmetrization" of a previously directed one, by using g.set_directed(False). Best wishes.

2 4