graph-tool January 2016

graph-tool@skewed.de

10 participants
20 discussions

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

g.vp["pos"]
by kevinc 28 Jan '16

28 Jan '16

g = load_graph('mydata.gml') state = gt.minimize_blockmodel_dl(g) b = state.b gt.graph_draw(g, inline=True, pos=g.vp["pos"], vertex_fill_color=b, vertex_shape=b, output="mydata.pdf") This leads to the following error: ----> 3 gt.graph_draw(g, inline=True, pos=g.vp["pos"], vertex_fill_color=b, vertex_shape=b, output="2013_blocks_mdl.pdf") /usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in __getitem__(self, key) 1419 p = self.properties[(self.t, key)] 1420 return p[p.get_graph()] -> 1421 return self.properties[(self.t, key)] 1422 1423 def get(self, key, default=None): KeyError: ('v', 'pos') My question is what g.vp["pos"] does? 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.

2 1

graph-tool Install problems [Mac OS X El Cap, Anaconda3-2.3, Python 3.4]
by Travis Earheart 28 Jan '16

28 Jan '16

I am trying to install graph-tool on a MacBook Pro with El Capitan using Anaconda3-2.3 which installs Python 3.4. I have tried installing all necessary supporting packages every way but Sunday. I have gone through every graph-tool mailing list archive, StackOverflow question, etc etc and cannot seem to get graph-tool installed correctly. Actually, I believe graph-tool installs correctly, it is perhaps a linking issue with Boost. If anyone has complete instructions for a fresh install I would almost rather do that. Regardless, here is the error I am receiving… >>> from graph_tool.all import * dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /Users/tearheart/anaconda/lib/python3.4/site-packages/graph_tool/libgraph_tool_core.so Expected in: /Users/tearheart/anaconda/lib/python3.4/site-packages/graph_tool/../../..//libboost_python3.dylib dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /Users/tearheart/anaconda/lib/python3.4/site-packages/graph_tool/libgraph_tool_core.so Expected in: /Users/tearheart/anaconda/lib/python3.4/site-packages/graph_tool/../../..//libboost_python3.dylib Any and all help is greatly appreciated. Travis Earheart Director, Analytics 720.907.0309 (D) | 858.699.5641 (M) travis.earheart(a)trueffect.com<mailto:travis.earheart@trueffect.com> www.trueffect.com<applewebdata://BA6AD399-300B-48FD-9462-294DF5EA8655/www.trueffect.com>

2 1

RuntimeError (Edge filter is active / vertex filter is not)
by François Kawala 13 Jan '16

13 Jan '16

Hello, Since past couple days I encounter a new RuntimeError that I fail to explain. See below the end of the error stack : File "utils/graph.py", line 345, in multiple_shortest_path p = graph.vertex(pred_map[v]) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1777, in vertex v = libcore.get_vertex(self.__graph, int(i), use_index) RuntimeError: Edge filter is active but vertex filter is not. This is a bug. This error is raised in a customized version of the *graph_tool.topology.shortest_path *function. This function (named multiple_shortest_path) is "optimized" to compute multiple shortest paths from a source vertex to a set of targets. This function is presented below. Would anybody have some hints on the reason of this intermittent error ? Thanks, F. def multiple_shortest_path(graph, source, targets, distances, pred_map): """ :param graph: a GraphTool.Graph instance. :param source: origin vertex id in *graph* :param targets: the vertices ids (in *graph*) for which we compute the shortest paths :param distances: a property map that contains distances from source vertex to each vertex :param* pred_map: a property map of predecessor computed by graph_tool.shortest_distance* """ # sort the targets from the farthest to the closest targets, _ = zip(*sorted([(graph.vertex(t), distances.a[t]) for t in targets], key=lambda x: x[1])) vlists = {} for tgt in targets: if pred_map[tgt] == int(tgt) and tgt != source: # Ain't no path to target (should not happen, but better safe than sorry) vlists[tgt] = [] v = tgt vlist = [tgt] # we crawl back the predecessor map until the source is reached while v != source: # one step more toward the source p = graph.vertex(pred_map[v]) if p in vlists: # we already know the shortest_path (avoid useless crawl back to the source) vlist = vlists[p] + vlist v = graph.vertex(vlist[0]) else: # saves the current step vlist.insert(0, p) # predecessor vertex becomes the current vertex (recall we crawl back from target until source) v = p # Saves the vertices list from target to source (ie. the shortest path wrt. the predecessor map) vlists[tgt] = vlist return vlists

2 1

Unsatisfiable dependency - Ubuntu 14.04LTS (trusty)
by François Kawala 13 Jan '16

13 Jan '16

Hello, The latest version of the trusty python-graph-tool package depends on : gcc-5-base (= 5.2.1-22ubuntu2) (caused by libgomp1); libstdc++6 (>= 5). However, these versions aren't backported to Ubuntu 14.04LTS (trusty). Is there a work around, or should I move to a non LTS Ubuntu version ? Thanks ! f

2 1

slow shortest path
by lei 13 Jan '16

13 Jan '16

I want to compute shortest path repeatedly, each time some edge weight is changed. The following implementation run very slowly, is this my problem? for e in elist: w=wt[e] wt[g.edge_index[e]]=sys.maxint d2=shortest_distance(g, g.vertex(s), g.vertex(t),weights=wt) wt[e]=w Profiling says most of the time (132 sec in 153 sec)is spend on __init__.py:539(__setitem__). It seems each time all weights are updated using wt, if there is a large number of edges, this will cost a lot time. But in my case, only one edge weight is changed, is there some other way to do this? Thanks.

2 2

Is it possible to use the graph-tool lib in c/c++ program
by hao 07 Jan '16

07 Jan '16

Hi, Since the graph-tool lib is implemented with c++, I am wondering is it possible to directly use this lib in c++ program? If yes, would any one give some instructions on how to do that? Thanks. Best Regards~ -- 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 January 2016