graph-tool February 2015

graph-tool@skewed.de

11 participants
22 discussions

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

Python<->C++ interface tutorial?
by maksimt 08 Apr '15

08 Apr '15

Hey, I'm a researcher without much experience in creating good graph algorithm implementations. I'm blown away with how much faster some algorithms are in C++ (for instance Dijkstra's shortest path) when compared to the implementation in python or matlab. Is there any chance you could create a tutorial of how you made the python interface to C++ code? Also as far as I can tell this is the best graph library out there, but it's relatively hard to install. As a result people like me are using inferior libraries for algorithms and visualization. Do you think you could work on making your library easier to install, or at least providing more instructions? I work with both Windows and Mac OS X, and I wasn't able to install your library on either. -- 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 8

rpm spec
by Gordon Messmer 24 Mar '15

24 Mar '15

I'm packaging graph-tool for RHEL. I'd like to contribute the spec for distribution so that your users can easily build packages on Red Hat systems, and you can offer them for distribution if you choose to do so. I did notice a couple of problems while packaging. First, your build scripts appear to install into the general library path(distutils.sysconfig.get_python_lib()) when it should install to the platform-dependent library path (distutils.sysconfig.get_python_lib(1)). According to the manual, I believe you should be using pyexecdir rather than pythondir. http://www.gnu.org/software/automake/manual/html_node/Python.html Second, numpy headers appear to be included incorrectly. >>> print numpy.get_include.__doc__ Return the directory that contains the NumPy \*.h header files. Extension modules that need to compile against NumPy should use this function to locate the appropriate include directory. $ python -c 'import numpy; print "-I" + numpy.get_include()' -I/usr/lib64/python2.7/site-packages/numpy/core/include However, arrayobject.h is included directly where the correct path should be numpy/arrayobject.h. Because the headers don't include that prefix, the spec file includes a static path for the headers. Similarly, the cairomm headers are included without a prefix. # pkg-config --cflags cairomm-1.0 -I/usr/include/cairomm-1.0 -I/usr/include/cairo -I/usr/include/sigc++-2.0 -I/usr/lib64/sigc++-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 cairommconfig.h is included, when the correct path is cairomm/cairommconfig.h.

2 5

Networkx VS graph-tool
by mohsenuss91 01 Mar '15

01 Mar '15

Hi, I'm working on graph mining, so I'm trying to find the best library to do that. I read in http://graph-tool.skewed.de/performance that "graph-tool" is faster, so I tried the same program who count the duplicated graphs (I call them frequent in the program) in networkx and graph-tool. graph are in this .txt file ==> http://pastebin.com/u5BUxx2p networkx program ==> http://pastebin.com/FPRy7Ywv graph-tool program ==> http://pastebin.com/dK93x6tf there are the results: * Networkx: RUNNING TIME: 0.00204300880432s Reading from file: 0.000211000442505s Algo: 0.00186109542847s ************* graph-tool: RUNNING TIME: 0.0780489444733s Reading from file: 0.00203204154968s Algo: 0.0760469436646s* ___________________________ I 'm not sure if my graph-tool program need amelioration or that is the best performance ? -- 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.

2 2

sfdp_layout force parameters
by pete 25 Feb '15

25 Feb '15

Hi there, After trying four other force-directed graph layout implementations, I was very happy to find graph-tool's sfdp_layout, which easily handles graphs with O(10^6) nodes while still offering a number of layout customizations. I'd like to better understand the intended effects of some of the sfdp_layout parameters. I've included below a script featuring a toy graph that I've been experimenting with. It seems that increasing C -- the relative strength of repulsive force -- doesn't have any effect on the layout. Meanwhile, increasing mu -- the strength of the attractive force -- seems to /reduce/ vertex clustering. Any insight into this behavior? Am I misunderstanding the documentation? Thanks, Pete ------------------------- import graph_tool.all as gt # specify graph as a sparse matrix garray = [(0, 1, 0.9), (0, 2, 0.9), (0, 4, 0.8), (0, 5, 0.8), (1, 2, 0.9), (2, 3, 0.6), (3, 6, 0.6), (4, 7, 0.8), (4, 8, 0.8), (4, 9, 0.8), (4, 10, 0.8), (5, 6, 0.7), (7, 8, 0.8), (7, 9, 0.8), (7, 10, 0.8), (8, 9, 0.8), (8, 10, 0.8), (9, 10, 0.8)] # get number of vertices N = max(line[1] for line in garray) + 1 # initialize graph and vertices g = gt.Graph(directed = False) g.add_vertex(N) # initialize edge property for weights weights = g.new_edge_property('double') # construct edges for line in garray: edge = g.add_edge( g.vertex(line[0]), g.vertex(line[1]) ) weights[edge] = line[2] # compute vertex positions # eweight = None edge weights # C = 0.2 relative strength of repulsive forces # K = None optimal edge length # p = 2 repulsive force exponent # gamma = 1.0 strength of attractive force between connected components, or group assignments # mu = 0.0 strength of attractive force between vertices of the same connected component, or group assignment # mu_p = 1.0 scaling exponent of attractive force between vertices of the same connected component, or group assignment pos = gt.sfdp_layout(g, eweight = weights, C = 0.2, K = None, p = 2, gamma = 1.0, mu = 0.0, mu_p = 1.0) # generate figure gt.graph_draw(g, pos, vertex_text = g.vertex_index, output_size = (200, 200), output = 'graph.png') -- 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.

2 1

String in properties
by mohsenuss91 23 Feb '15

23 Feb '15

Hi, how to put a label ()string in vertex or edge properties ? I can only find: new_vertex_property("int") and new_edge_property("int") -- 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.

2 1

how to install "graph-tool" in UBUNTU 12.04 LTS 32 bits and windows7
by mohsenuss91 23 Feb '15

23 Feb '15

Hi, I'm trying to install "graph-tool" in UBUNTU 12.04 LTS 32 bits and windows7 but I have some problems. I cant find the method for windows7 and for ubuntu when I make: apt-get install python-graph-tool I get something like: Les paquets suivants contiennent des dépendances non satisfaites : python-graph-tool : Dépend: libboost-graph1.54.0 mais il n'est pas installable Dépend: libcgal10 mais il n'est pas installable E: Impossible de corriger les problèmes, des paquets défectueux sont en mode « garder en l'état ». How to solve this please! -- 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.

2 1

Paths crossing in sfdp layout
by luistavares 19 Feb '15

19 Feb '15

Please, I would like to know if there is a way to ensure that the paths in my graph will not cross. I'm using sfdp layout with a tree graph and I set the parameters cooling_step to 0.99 and epsilon to 1e-4. Thanks for any help. <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- 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.

1 0

Button listeners - a simple way to do it
by podro182 13 Feb '15

13 Feb '15

I wanted to make a snippet, that does the following: It shows a BFS tree of length 1 and when you click on a node it shows the BFS of the clicked node. Is there a simple way to do it by using the graph_draw method? -- 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.

2 3

in_neighbours() of undirected graphs are always empty
by james 13 Feb '15

13 Feb '15

Hi Tiago, I'm using graph-tool 2.2.36 with boost 1.57.0. I just found out that in_neighbours() for undirected graphs are always empty. Is this intended or a bug? Here's what I tried: Thank you! James -- 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.

2 1

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graph-tool February 2015