November 2012 - 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

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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

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Undefined symbol drawing function
by sasho.j.markov 20 Apr '15

20 Apr '15

Hi New to the graph-tool. Build it from src on Fedora 16 (64) . Built with cairomm enabled . Try to run as per the quick start , however when executing graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ... output_size=(200, 200), output="two-nodes.pdf") i get undefined symbol _ZN5Cairo7ContextC1EP6_cairob However the symbol above is defined in : libcairomm-1.0.so see below nm command results nm /usr/local/lib/libcairomm-1.0.so | grep -i _ZN5Cairo7ContextC1EP6_cairob 0000000000014b90 T _ZN5Cairo7ContextC1EP6_cairob Interestingly the library libgraph_tool_draw.so has indeed have the undefined symbol U _ZN5Cairo7ContextC1EP6_cairob but does not depend on the cairomm libarary - see the ldd output . unless the library is dynamically load i do not understand why Any advise appreciated- regards Sasho ldd /usr/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so linux-vdso.so.1 => (0x00007fffc46da000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f99fd6cd000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f99fd30e000) libboost_iostreams.so.1.49.0 => /usr/local/lib/libboost_iostreams.so.1.49.0 (0x00007f99fd0f6000) libboost_python.so.1.49.0 => /usr/local/lib/libboost_python.so.1.49.0 (0x00007f99fceaa000) libboost_regex.so.1.49.0 => /usr/local/lib/libboost_regex.so.1.49.0 (0x00007f99fcbc8000) libCGAL.so.9 => /usr/local/lib/libCGAL.so.9 (0x00007f99fc9a5000) libexpat.so.0 => /usr/local/lib/libexpat.so.0 (0x00007f99fc77c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f99fc54d000) libm.so.6 => /lib64/libm.so.6 (0x00007f99fc2c9000) libc.so.6 => /lib64/libc.so.6 (0x00007f99fbf11000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99fbcfb000) /lib64/ld-linux-x86-64.so.2 (0x00000030cea00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99fbadf000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f99fb8db000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f99fb6d7000) libz.so.1 => /lib64/libz.so.1 (0x00007f99fb4c0000) librt.so.1 => /lib64/librt.so.1 (0x00007f99fb2b8000) libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x00007f99fb0b3000) libboost_thread.so.1.49.0 => /usr/local/lib/libboost_thread.so.1.49.0 (0x00007f99fae98000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007f99fac41000) -- 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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Parallel Processing
by Derek Ditch 21 Nov '13

21 Nov '13

I want to use graph-tool using the multiprocessing library in Python 2.6. I keep running into issues though with trying to share a full graph object. I can store the graph in a multiprocessing.Namespace, but it doesn't keep the dicts of properties. Example: def initNS( ns ): _g = Graph( directed = False) ns.graph = _g ns.edge_properties = { 'genres': _g.new_edge_property("vector<string>"), 'movieid': _g.new_edge_property("int"), } ns.vertex_properties = { 'personid': _g.new_vertex_property("int32_t") } """ Build property maps for edges and vertices to hold our data The graph vertices represent actors whereas movies represent edges """ # Edges _g.edge_properties["genres"] = ns.edge_properties['genres'] _g.edge_properties["movieid"] = ns.edge_properties['movieid'] # Vertices _g.vertex_properties["personid"] = ns.vertex_properties['personid'] ns.graph = _g ########## This initializes 'ns', which is a multiprocessing.Namespace. The problem is that for example, ns.edge_properties[ * ] tells me that the type isn't pickle-able. I tried to just skip that and use the _g.edge_properties to access it, but those dicts aren't carried over to the different process in the pool. Presumably b/c they aren't pickle-able. Any thoughts about how to fix this? (For those interested, I'm attempting to use the IMDbPy library to do some graph analysis on the relationships among actors and movies. Each process has it's own db connection and trying to populate the graph with actor and movie information in parallel since it's a pretty large and dense graph. Somewhere in the neighborhood of 250,000+ vertices for just a depth of three relationships) Thanks, -- Derek

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Drawing large graphs
by alepulver 03 Dec '12

03 Dec '12

Hello, I've started using graph-tool mainly because it's faster than networkx. Recently I tried analyzing Wordnet by constructing a graph from all synsets and polysemy relations between them; it has 117659 nodes and 549414 edges. When I run statistics such as degree average, local clustering average and pseudo diameter they only take a few seconds. On the other hand, if I try to draw it with graph_draw it takes 6 hours (using 4 cores, and about 24hs of combined CPU time) or graphviz_draw (which I haven't run for more than an hour). Initially I thought the bottleneck was in using labels (which I removed afterwards), then in the layout algorithm (before confirming that random layout takes only a few seconds), and finally outputting pixels instead of vectors (svg instead of png), but none of them seemed to have to do with it. Also, saving the graph also takes just a few seconds. I have uploaded it in xml.gz format here (it's 6.4MB): http://www.sendspace.com/file/zc7yrh If you have any suggestions please let me know. Thanks in advance, Alejandro -- 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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Any way to not compiling source code?
by Qiang Ren 21 Nov '12

21 Nov '12

Hi ,all I have been using graph_tool for a few months. I finished compiling it in Archlinux in 4G memory, but failed to compile in Ubuntu linux in 4G memory. I wonder if there exists some way to directly use the library without compiling source code. Or , what have been done during the compiling of graph_tool? How can we use the post-compile files in another computer? Advise on same operating system or different operating system are both OK. Thank you all!

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Segmentation fault (core dumped)
by Padraig 19 Nov '12

19 Nov '12

Hi, I just compiled graph-tool 2.2.17 from source under Ubuntu 12.10. When I enter the command 'import graph_tool' in the python interpreter everything appears to be working fine. Whoever when I create a python script (say test.py) containing the command 'import graph_tool' and attempt to run this script from the terminal (using the command python test.py) I get the error 'Segmentation fault (core dumped)'. I would really appreciate any help with this problem Regards, Padraig -- 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.

4 13

Problems installing
by Hugo Leeney 15 Nov '12

15 Nov '12

I use pythonbrew, venv and pip mostly for python dev - I am a relative novice. I've spent some time trying to get graph-tool installed and have failed badly. I have downloaded the src (graph-tool-2.2.18) and can not ./configure . I am on Debian squeeze and have tried with apt-get's boost and with a built-from-source boost but always get the same error - as shown below. Versions of python and exact checks vary depending on environment and options to configure. Below is with a 2.7.2 python environment and this command "./configure --with-boost-python=/home/hleeney/usr/local/lib/libboost_python.a". Any help is greatly appreciated. =========================== Using python version: 2.6.6 =========================== checking for boostlib >= 1.38.0... yes checking whether the Boost::Python library is available... yes checking for exit in -l/home/hleeney/usr/local/lib/libboost_python.a... no checking for exit in -l/home/hleeney/usr/local/lib/libboost_python.a-py2.6... no checking for exit in -l/home/hleeney/usr/local/lib/libboost_python.a-2.6... no checking for exit in -lboost_python-/home/hleeney/usr/local/lib/libboost_python.a... no checking for exit in -lboost_python-/home/hleeney/usr/local/lib/libboost_python.a-py2.6... no checking for exit in -lboost_python-/home/hleeney/usr/local/lib/libboost_python.a-2.6... no checking for exit in -lboost_python... no checking for exit in -lboost_python-py2.6... no checking for exit in -lboost_python-2.6... no checking for exit in -lboost_python-mt... no checking for exit in -lboost_python-mt-py2.6... no checking for exit in -lboost_python-mt-2.6... no configure: error: No usable boost::python found

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Create Graph from Missing Edges
by cc 01 Nov '12

01 Nov '12

Hello everyone, I'm curious as to whether it is possible to compare two graphs (g2 and g1) and build a graph object from the edges g2 has but g1 misses? In other words, create a graph object out of the edges in g2 that are unique to it compared to the edges in g1, given that both g1 and g2 have sources and targets that are the same. Ideally, it would be interesting to see how to do that regardless of whether someone is a source or a target in either graph (undirected). I know there is likely an involved way of doing this, but I'm wondering whether there is a novel approach to take. Any ideas? Thank you for your time. -- 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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