graph-tool April 2016

graph-tool@skewed.de

12 participants
19 discussions

find community classes/labels
by yinjunjun 04 Jul '16

04 Jul '16

Hi, I am trying to use graph tool to extract communities, and I used the minimize_blockmodel_dl function. However, after it has been executed successfully, I wish to know each vertex and information of which community it belongs to, and I can not figure out how. For example, state = graph_tool.community.minimize_blockmodel_dl(g, parallel=True) ##print state.b print state.get_blocks().get_array() it give me an array of all the vertex in zero. Could any one point me to the right directions. Thank you very much. Best Regards Junjun -- 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 see the relations between two groups of blocks in a bipartite network?
by Andrea Briega 25 Apr '16

25 Apr '16

Hi, Sorry if I ask basic questions but I'm new in this. I have a bipartite network, with two types of nodes with no connections between the nodes of the same type, only between different types. I have run minimize_blockmodel_dl y minimize_nested_blockmodel_dl with different options but I always get separated blocks for each type of node: some blocks only with nodes of one type and the rest only with nodes of the other type. But I am really interested in the relation between this two groups of blocks. Any idea about how could I get that? Thank you very much. Best regards, Andrea

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First question - Planarity
by Matyas, Csongor 24 Apr '16

24 Apr '16

I will also post my first question, this was the main reason why I registered for this mailing list. The description and examples were usually more than enough for me to use graph_tool, nice job ;) I have a question though. In the "graph_tool.topology.is_planar(*g*, *embedding=True*)" how do I use the embedding information to print my graphs planar. Do I have to do that for myself, or there is a built in function that I didn't find? Do I have to add the edges following the order that they come using the embedding somehow? If there is no option for this in graph tool any help or idea, tip or trick is greatly appreciated. I've tried to use the Kuratovski, but it won't print them planar, also tried the maximal planar option, didn't help. Thank you very much Csongor The adjacency matrix of an example of my graphs can be seen below: (0, 3) 1.0 (0, 11) 1.0 (1, 0) 1.0 (2, 1) 1.0 (3, 2) 1.0 (3, 6) 1.0 (4, 7) 1.0 (4, 23) 1.0 (5, 4) 1.0 (6, 5) 1.0 (7, 2) 1.0 (7, 6) 1.0 (8, 5) 1.0 (8, 11) 1.0 (9, 8) 1.0 (9, 14) 1.0 (10, 9) 1.0 (11, 10) 1.0 (12, 15) 1.0 (12, 19) 1.0 (13, 10) 1.0 (13, 12) 1.0 (14, 13) 1.0 (15, 14) 1.0 (16, 15) 1.0 (16, 19) 1.0 (17, 16) 1.0 (17, 22) 1.0 (18, 17) 1.0 (19, 18) 1.0 (20, 1) 1.0 (20, 23) 1.0 (21, 18) 1.0 (21, 20) 1.0 (22, 21) 1.0 (23, 22) 1.0

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Introduction
by Matyas, Csongor 20 Apr '16

20 Apr '16

Hi everyone My name is Csongor Matyas. I'm a hungarian PhD student studying in St. John's Canada. I'm working with knots, trying to approach them from graph theory point of view. I'm using python and this is how I found graph_tool. I like it, thank you all ;) Csongor

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Anaconda Release
by Johannes Hoppe 20 Apr '16

20 Apr '16

Hi, I noticed problems with the Ubuntu release, not to mention the trouble one would have to go through to make this work on Windows. As a result the only simple way to get graph-tool working is on OSX with brew. Which makes it virtually inaccessible for people living in countries with a GDP that doesn't by everyone a shiny MacBook. Furthermore there is currently no way to have it onto a production system except for docker. Which to be fair is my personal concern. Anaconda or just conda, has been around for a while now. In case you don't know it, it's a cross platform package manager. Like apt-get but on linux, osx and windows. It will allow you to even get a compiler inside a virtual environment. Most of the dependencies are already available on conda, therefore it should be rather simple to get graph-tool on there as well. As a added bonus, you can even vendor dependencies (maybe good for boost). There have been already some efforts by people like Alexey Strokach to delivery graph-tool on conda. (https://anaconda.org/ostrokach/graph-tool) It would be great tho, to get some official support. I must admit, I don't have much experience with releasing packages on conda. I still think its worth looking into for a couple of reasons: \- Support for all OS \- Support for multiple python versions (not only the systems default) \- single command install Please let me know what you thing about this idea? I'd be willing to invest some time into that, but only if it is your interest. Cheers, Joe \-- **Johannes Hoppe** Lead Software Engineer [johannes.hoppe@thermondo.de](mailto:johannes.hoppe@thermondo.de) **°Thermondo **- Der Heizungsbauer. **We are hiring: [www.thermondo.de/jobs/](http://www.thermondo.de/jobs/)** [www.thermondo.de](http://www.thermondo.de/) | Thermondo GmbH, Brunnenstr. 153, 10115 Berlin Eingetragen in Berlin unter: HRB 129321 I Steuernummer: 30/557/33244 Geschäftsführer: Florian Tetzlaff, Philipp A. Pausder | USt-IdNr.: DE273951924 [Facebook](https://www.facebook.com/thermondo) | [Google+](https://plus.google.com/+ThermondoDe/posts) | [Twitter](https://twitter.com/thermondo) | [Youtube](https://www.youtube.com/channel/UCaM56yLLGe4y4qohjjKFAYA)

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Installation under Ubuntu 14
by Yannis Haralambous 13 Apr '16

13 Apr '16

Hi, I'm trying to install graph-tool under Ubuntu 14. I didn't found gcc5 in the list of synaptic packages but I did installed clang3.4. But when I run ./configure, it doesn't find clang3.4 (and probably detects pre-installed gcc 4.8.2 instead). How can I tell ./configure to use clang3.4 rather than gcc4.8.2 ? Thanks in advance Yannis -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous(a)telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)

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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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OS X Macports clang with openmp build of graph-tool
by Steve 05 Apr '16

05 Apr '16

Macports clang 3.7 and 3.8 now support openmp, which creates the opportunity to build graph-tool on OS X with OpenMP speeds.I've tried the following, which haven't quite worked yet, but it's close. Any pointers would be appreciated. sudo port uninstall py-graph-tool py27-graph-tool sudo port clean --dist py-graph-tool py27-graph-tool sudo port install clang-3.8 +openmp sudo port -d install py-graph-tool py27-graph-tool configure.compiler=macports-clang-3.8 configure.args=--enable-openmp I expected the option "configure.args=--enable-openmp" would tell the autoconf'd ./configure command to specify --enable-openmp, but it does not: DEBUG: Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-graph-tool/py27-graph-tool/work/graph-tool-2.13" && ./configure --prefix=/opt/local --with-boost=/opt/local --exec-prefix=/opt/local/Library/Frameworks/Python.framework/Versions/2.7 … checking whether to enable parallel algorithms with openmp... no The port notes for clang-3.8 say: Use with clang-3.[78] (when built with +openmp variant) by adding "-fopenmp" to your compile and link lines. (Or "-I/opt/local/include/libomp -L/opt/local/lib/libomp -fopenmp" if clang is installed without +openmp.) Based on the Port Phases <https://guide.macports.org/chunked/reference.phases.htm> page, I've tried a variety of options like configure.cxxflags-append=-fopenmp, all without success. Perhaps a custom portfile is necessary, but this would be easiest to address through the port command line. -- 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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Triangle Counting
by Stephen Bonner 04 Apr '16

04 Apr '16

Is there a primitive function for counting triangles in graph-tool? Currently i am explicitly creating a triangle graph and then using the motif function to search for this graph. - triangle = Graph() v1 = triangle.add_vertex() v2 = triangle.add_vertex() v3 = triangle.add_vertex() e = triangle.add_edge(v1, v2) e = triangle.add_edge(v1, v3) e = triangle.add_edge(v3, v2) triangle.set_directed(False) motifsgraph, num_triangles = motifs(tempG, 3, motif_list=[triangle]) Just wondering if there is a better way to do this as it is 1) slow and 2) turning up some strange results. Many Thanks, Rob

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graph-tool April 2016