February 2018 - graph-tool - archives.skewed.de

Understanding the Model Function for Generative model
by ashutosh 27 Feb '18

27 Feb '18

With the reference to the paper on the generative models ---- " https://arxiv.org/pdf/1705.10225.pdf " It is supposed to be an introductory publication on the generative model idea used in graph-tool but I am having little difficulty in understanding the equation 4, the model generating function using Lagrange Multiplier. A little more explanation of how this equation arrived, will be very much helpful. A reference to further reading to understand this will also be very helpful. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Comiling error of graph tool
by Noriyuki Kojima 24 Feb '18

24 Feb '18

Hello, I am encountering the compiling issue of graph-tool 2.26 (latest version.), when I run command "make -j 16" I am using, gcc 5.4.0 boost: 1.66 python: 3.5 (anaconda distribution) os: CentOS7 Output of "make -j 16" is attached as out.txt. Output of Configure, using commands "./configure CXX="/sw/arcts/centos7/gcc/5.4.0/bin/g++" LDFLAGS="-L/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib" CPPFLAGS="-I/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib" --with-python-module-path="/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages" --prefix="/home/kojimano/anaconda3/envs/CogMap2/lib" --with-boost="/scratch/jiadeng_fluxoe/kojimano/packages/one_six" -with-boost=yes --disable-cairo --disable-sparsehash " is attched as out_config.txt, config.log. -- Noriyuki, Kojima University of Michigan, Engineering Computer Science kojimano(a)umich.edu

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speed of all_neighbours
by Howmahgee 14 Feb '18

14 Feb '18

I am new to graphtool but super excited by what I have implemented so far. I have a question however about the speed of the all_neighbors method. >From trying it on various machines, it seems that it takes around 0.01s for v.all_neighbors() where v is an arbitrary vertex. I have tried this on a 4 node graph and a 2M node graph getting the same result. Has anyone else found the same thing? It seems to me to be particularly slow. Storing a graph as an adjacency list in a hashtable should have microsecond look up time, I assumed graph-tool stored the graph in such a way but I haven't yet come across the place where the architecture it is described. At any rate, am I doing something wrong or is 0.01s the expected look up time? I am trying to build a list of "friends of friends" on a graph of around 2M nodes 200M edges, so if all_neighbors takes 0.01s, then to get "friends of friends" takes about 1s for each node....which prohibits traversing the graph in this way in a reasonable time Nk -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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graph-tool on CentOS?
by P-M 08 Feb '18

08 Feb '18

Dear all, I know there has been some discussion on the mailing list from a few years ago of getting graph-tool to run on CentOS which, based on a quick read, seems to have concluded that it was difficult. I was wondering if people had any experiences with the current state of play on that front. Has the situation changed? Can I, in people's opinion, be confident that I can get the latest version of graph-tool to run on CentOS without having to spend large amounts of time trying to get it to work each time I need to update the version? For context: I am having to rebuild my Ubuntu machine and it was suggested I should look into moving to CentOS instead. I am unfamiliar with CentOS but if graph-tool will be difficult to get to run on CentOS then that would be a good reason for me not to move to CentOS. (Obviously there may be other reasons for moving to CentOS but those are not my primary concern here.) Thank you for any opinions on this topic in advance! With best wishes, Philipp -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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make graph from scipy sparse matrix
by hoptical 07 Feb '18

07 Feb '18

hi, I have a scipy sparse matrix and I want to make a graph from this matrix in graphtool. In Netwrokx this is simplly done by from_scipy_sparse_matrix method(). is there any method like this in graph tool package? tnx. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Grouping and drawing
by Mátyás Csongor 07 Feb '18

07 Feb '18

Is there an example that uses multiple groups within the graph and draw it accordingly. I have multiple groups and I would like to draw the graph in a way that all vertices within each group to be close to each other. I could not achieve this with a problem that has a known solution, so I thought maybe it is not possible, or if it is, someone could help me in how I should try doing it. The test problem that I've chosen is to take all amino acids, organize them into groups according to their properties, and to get to this planar grouping: https://www.researchgate.net/publication/11265315/figure/fig1/AS:2812510187… I would like some general help ideas, but if someone would like to join me in this small project, I can share what I've tried until now. Csongor

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Running all_shortest_path on large graph
by Evangelos Petsalis 06 Feb '18

06 Feb '18

Hi, I have a large graph (800K vertices and 6e6 edges) and I am running the all_shortest_paths function with edge weights. The problem is that due to the size of the graph, there are probably millions of paths that qualify and the function fails with a "MemoryError" code. Is there a way to limit the number of shortest paths returned, or even better a version that returns an iterator and compute the paths as needed? Thanks -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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