graph-tool June 2012

graph-tool@skewed.de

8 participants
17 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

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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

5 9

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.

3 3

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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(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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Re: [graph-tool] graph-tool - Undefined symbol drawing function
by Sasho Markov 30 Jun '12

30 Jun '12

Hi Tnx for the response . As per the request i have enclosed the config .log and config Regards sasho markov On 27 Jun 2012, at 8:00 PM, graph-tool-request(a)skewed.de wrote: > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. Undefined symbol drawing function (sasho.j.markov) > 2. Re: Undefined symbol drawing function (Tiago de Paula Peixoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Jun 2012 10:55:54 -0700 (PDT) > From: "sasho.j.markov" <sasho.j.markov(a)gmail.com> > To: graph-tool(a)skewed.de > Subject: [graph-tool] Undefined symbol drawing function > Message-ID: <1340733354608-4024728.post(a)n3.nabble.com> > Content-Type: text/plain; charset=us-ascii > > 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. > > > ------------------------------ > > Message: 2 > Date: Tue, 26 Jun 2012 20:30:53 +0200 > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: Main discussion list for the graph-tool project > <graph-tool(a)skewed.de> > Subject: Re: [graph-tool] Undefined symbol drawing function > Message-ID: <4FE9FFDD.3000703(a)skewed.de> > Content-Type: text/plain; charset="utf-8" > > On 06/26/2012 07:55 PM, sasho.j.markov wrote: >> 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 > > Very strange indeed. Could you please send the entire output of the > configure command, as well as the config.log file? > > Cheers, > Tiago > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > > > >

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nan egde betweenness values
by Padraig 29 Jun '12

29 Jun '12

Hi, I am computing a centrality.betweenness for a graph with weight equal to an edge property map of type double. Some of the resulting edge betweenness values are nan. The graph in question is connected so am unsure why a nan value is occurring. I would be delighted to hear any suggestions. 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.

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How to use the public key in Ubuntu 12.04
by Qiang Ren 28 Jun '12

28 Jun '12

Hi, all friends! I want to install graph_tool in Ubuntu 12.04. I add the source to my sources.list and update the source. It replys "W: GPG error: http://downloads.skewed.de oneiric Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 697EC21F15F95514" I don't know how to add the public key. I tried to save F36FE35D<http://pgp.skewed.de:11371/pks/lookup?op=get&search=0x04DC461EF36FE35D>in keyfile and "sudo apt-key add keyfile" . But it says"gpg: no valid OpenPGP data found." What is this problem? Thank you for your suggestion. 2012/6/26 <graph-tool-request(a)skewed.de> > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. Re: Re ?What GNU/Linux distribution do you have, Debian or > Ubuntu? What version? (Tiago de Paula Peixoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Jun 2012 10:47:46 +0200 > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: Main discussion list for the graph-tool project > <graph-tool(a)skewed.de> > Subject: Re: [graph-tool] Re ?What GNU/Linux distribution do you have, > Debian or Ubuntu? What version? > Message-ID: <4FE97732.10009(a)skewed.de> > Content-Type: text/plain; charset="utf-8" > > Hi, > > I've released a new version of graph-tool (2.2.17). Could you please try > again > with apt-get? > > I tried it on an ubuntu machine, and everything worked nicely... > > Cheers, > Tiago > > On 06/15/2012 02:40 PM, ?? wrote: > > My linux version?Ubuntu 12.04 > > GCC version?4.7 > > My problem comes up when compiling /layout/graph_sfdp. > > > > I have tried to used arch linux instead, but everything messed up when > configuring network :( > > > > 2012/6/15 <graph-tool-request(a)skewed.de <mailto: > graph-tool-request(a)skewed.de>> > > > > Send graph-tool mailing list submissions to > > graph-tool(a)skewed.de <mailto:graph-tool@skewed.de> > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://lists.skewed.de/mailman/listinfo/graph-tool > > or, via email, send a message with subject or body 'help' to > > graph-tool-request(a)skewed.de <mailto: > graph-tool-request(a)skewed.de> > > > > You can reach the person managing the list at > > graph-tool-owner(a)skewed.de <mailto:graph-tool-owner@skewed.de > > > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of graph-tool digest..." > > > > > > Today's Topics: > > > > 1. (no subject) (??) > > 2. Re: (no subject) (Tiago de Paula Peixoto) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 14 Jun 2012 20:29:11 +0800 > > From: ?? <renq654321(a)gmail.com <mailto:renq654321@gmail.com>> > > To: graph-tool(a)skewed.de <mailto:graph-tool@skewed.de> > > Subject: [graph-tool] (no subject) > > Message-ID: > > <CAM7UdKggw3JcoV3wpxSEU2ygD9Fh0MO5SK2hV9mPhbLR= > wPa1w(a)mail.gmail.com <mailto:wPa1w@mail.gmail.com>> > > Content-Type: text/plain; charset="iso-8859-1" > > > > 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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Re ：What GNU/Linux distribution do you have, Debian or Ubuntu? What version?
by 任强 26 Jun '12

26 Jun '12

My linux version：Ubuntu 12.04 GCC version：4.7 My problem comes up when compiling /layout/graph_sfdp. I have tried to used arch linux instead, but everything messed up when configuring network :( 2012/6/15 <graph-tool-request(a)skewed.de> > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. (no subject) (??) > 2. Re: (no subject) (Tiago de Paula Peixoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Jun 2012 20:29:11 +0800 > From: ?? <renq654321(a)gmail.com> > To: graph-tool(a)skewed.de > Subject: [graph-tool] (no subject) > Message-ID: > <CAM7UdKggw3JcoV3wpxSEU2ygD9Fh0MO5SK2hV9mPhbLR=wPa1w(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > 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. >

2 1

ImportError: No module named graph_tool.all
by 任强 14 Jun '12

14 Jun '12

Hi, I am new in using graph_tool.After I have installed graph_tool,it shows"No module named graph_tool.all" I don't know how to solve this problem. I think I have successfully generated the makefile and correctly compiled it. Attached file 2nd is the output when I compiled the graph_tool. Attached file 3rd is the output when I configured graph_tool. I have tried many times,but it still doesn't work.Who can help me? Thanks a lot.

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graph-tool June 2012