October 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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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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Re: [graph-tool] Welcome to the "graph-tool" mailing list
by Ronnie Ghose 27 Oct '12

27 Oct '12

Sorry i'm new here. Is the code hosted on github? On 17 October 2012 17:13, <graph-tool-request(a)skewed.de> wrote: > Welcome to the graph-tool(a)skewed.de mailing list! > > To post to this list, send your message to: > > graph-tool(a)skewed.de > > General information about the mailing list is at: > > http://lists.skewed.de/mailman/listinfo/graph-tool > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > > http://lists.skewed.de/mailman/options/graph-tool/ronnie.ghose%40gmail.com > > > You can also make such adjustments via email by sending a message to: > > graph-tool-request(a)skewed.de > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe without confirmation. It is: > > epfisono > > Normally, Mailman will remind you of your skewed.de mailing list > passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. >

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Re: [graph-tool] Any way to not compiling source code?
by Tiago de Paula Peixoto 19 Oct '12

19 Oct '12

On 10/19/2012 12:00 PM, Guillaume Gay wrote: > Hi, > > I tried to do so, but configure fails. My understanding is I would also need to compile at least the boost libs against gcc-4.7 . Unfortunately I am a bit short on time now, and since the previously mentioned hack worked ... also the latest Arch linux ships whith gcc 4.7 and graph_tool was reported to compile with this setup, so I think your suspicions about gcc4.6 being responsible are sound. > > Sorry I'm not much more help right now, I'll try to go back to this when the my work stack is thinner ;). > Take your time, of course... :-) I'm just pointing out possible solutions. But note that you do not have to recompile boost or anything else if you switch compiler versions, since they are ABI compatible. Cheers, Tiago -- Tiago de Paula Peixoto <tiago(a)skewed.de>

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installation problems using macports on Mountain Lion
by hajons 18 Oct '12

18 Oct '12

Hi, When trying to install graph-tool on Mac OS 10.7.5, port 2.1.2, XCode 4.3.2 it fails with errors like this: :info:build In file included from graph_eigenvector.cc:24: :info:build ./graph_eigenvector.hh:44:23: error: no matching constructor for initialization of 'boost::unchecked_vector_property_map<long double, boost::vec_adj_list_vertex_id_map<boost::no_property, unsigned long> >' :info:build CentralityMap c_temp(vertex_index, num_vertices(g)); :info:build ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Please see attached log file. main.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Any help to solve this would be appreciated. Regards, Håkan -- 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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find_edge() Match
by mstcamus 15 Oct '12

15 Oct '12

Hi everyone, Does anyone have a way to use the find_edge() function to match edges based on whether the parameter property contains a value as opposed to a complete match? E.g., whether edges contain '2008' as opposed to something like 'Thu May 15 06:07:27 UTC 2008'. I looked at the source code in the latest git version, and it looks I'm limited to a direct match (for strings), but I wonder if anyone has any suggestions for how we can improve this code to match based on a substring? Could be handy. 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.

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(no subject)
by 任强 08 Oct '12

08 Oct '12

HI everyone! I have tried to install graph_tool by compiling source code.But for many times , it reports: virtual memory exhausted: Cannot allocate memory My PC has a 4G main memory and Intel i5 CPU.I thought 4G is enough. Then I tried to install by apt-get, and came up with a problem. I have already installed these library before, and versions are right. graph-tool : Depends: libboost-iostreams1.42.0 (>= 1.42.0-1) but it is not installable Depends: libboost-python1.42.0 (>= 1.42.0-1) but it is not installable Depends: libboost-regex1.42.0 (>= 1.42.0-1) but it is not installable Depends: libcgal5 but it is not installable Depends: libpython2.6 (>= 2.6) but it is not installable Depends: libboost1.42-dev but it is not installable Can anyone help me ? By the way,how to use the public key ? I have tried "apt-key add signature.asc",but it reports: gpg: no valid OpenPGP data found.

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