graph-tool December 2014

graph-tool@skewed.de

12 participants
19 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.

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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.

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Cannot pickle graph
by Helen Lampesis 29 Dec '14

29 Dec '14

Hi everyone, The following code snippet gives me a TypeError and I am wondering if you have any suggestion. ------------------------------------------------ import graph_tool as gt import pickle g = gt.Graph() pickle.dump(g, open('test_file', 'w’)) ------------------------------------------------ The error: TypeError: coercing to Unicode: need string or buffer, _io.BytesIO found I am working on Yosemite OS with graph_tool 2.2.35 (installed via macports). Thank you very much and happy new year!! Helen

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assiacpge2011@gmail.com veut vous suivre. Accepter ?
by assiacpge2011＠gmail.com 23 Dec '14

23 Dec '14

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1 0

Lattice layout
by marklasta 18 Dec '14

18 Dec '14

Hi there, I'm working with the "graph_tool.generation.lattice" on a 2D lattice visualization. Can you help me to draw a lattice graph, as in the documentation, but not rotated ? Thanks in advance. -- 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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make build error in Graphtool
by researcher 10 Dec '14

10 Dec '14

I have successfully configured the graph tool but where I try to build with ./make command I am getting the following error [root@localhost graph-tool-2.2.35]# make make all-recursive make[1]: Entering directory `/root/Desktop/graph-tool-2.2.35' Making all in src make[2]: Entering directory `/root/Desktop/graph-tool-2.2.35/src' Making all in graph make[3]: Entering directory `/root/Desktop/graph-tool-2.2.35/src/graph' Making all in centrality make[4]: Entering directory `/root/Desktop/graph-tool-2.2.35/src/graph/centrality' CXX graph_betweenness.lo CXX graph_centrality_bind.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo CXX graph_trust_transitivity.lo CXXLD libgraph_tool_centrality.la /usr/bin/ld: cannot find -l/usr/include collect2: error: ld returned 1 exit status make[4]: *** [libgraph_tool_centrality.la] Error 1 make[4]: Leaving directory `/root/Desktop/graph-tool-2.2.35/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/root/Desktop/graph-tool-2.2.35/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/Desktop/graph-tool-2.2.35/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/Desktop/graph-tool-2.2.35' make: *** [all] Error 2 [root@localhost graph-tool-2.2.35]# I am using following operating system and library packages with versions Centos 7 Gcc 4.8.2 BOOST 1_57.0 Python 2.7.5 CGAL 4.5 Expat2.1.0 Gmp 6.00 I have run ./configure --disable-cairo --disable-sparsehash Could you please help me out? The config.log file is attached I have already tried the following: make maintainer-clean autoreconf --force --install ./configure make Many Thanks in advance config.log <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.

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./configure error Graphtool
by researcher 09 Dec '14

09 Dec '14

Hi I am trying to install graphtool 2.2.35, I have installed all required library and verified that it is working. However when I run ./configure then I got the following error: checking: : : Using python version: 2.7.5 =========================== checking for boostlib >= 1.53.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking whether the Boost::Iostreams library is available... yes checking for exit in -lboost_iostreams... no checking for exit in -lboost_iostreams... (cached) no checking for exit in -lboost_iostreams-mt... no checking for exit in -lboost_iostreams-mt-py2.5... no checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking for main in -lCGAL... no checking whether to cgal debbuging with valgrind...... no checking python module: numpy... yes checking for /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking /usr/lib64/python2.7/site-packages/scipy/weave/scxx/object.h usability... yes checking /usr/lib64/python2.7/site-packages/scipy/weave/scxx/object.h presence... yes checking for /usr/lib64/python2.7/site-packages/scipy/weave/scxx/object.h... yes checking expat.h usability... yes checking expat.h presence... yes checking for expat.h... yes *checking CGAL/version.h usability... no config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> checking CGAL/version.h presence... no checking for CGAL/version.h... no configure: error: CGAL headers not found* I have attached the config.log file I am using Linux centos 7 GCC 4.8 Boost 1_57_.0 Pyhton 2.7.5 CGAL 3.5 GMP 6 Could you please help me out? I have already spent twoo much time too figure it out bu no luck. your help in this regard would highly be appreciated -- 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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Problems in bellman_ford_search (OverflowError and TypeError)
by Alessandro 08 Dec '14

08 Dec '14

Hello,I want to try graph-tool because it seems a very powerful and fast way to work with graphs in python. I installed it with the pre-compiled package for ubuntu 14.04 on a 32 bit machine. I tested this code from graph_tool.all import * g = Graph()v1 = g.add_vertex()v2 = g.add_vertex()v3 = g.add_vertex()v4 = g.add_vertex()v5 = g.add_vertex() e1 = g.add_edge(v1, v5)e2 = g.add_edge(v2, v3)e3 = g.add_edge(v3, v4)e4 = g.add_edge(v4, v2)e5 = g.add_edge(v4, v5)e6 = g.add_edge(v4, v1) weights = g.new_edge_property("int")weights[e1] = 2weights[e2] = 3weights[e3] = 2weights[e4] = -1weights[e5] = 5weights[e6] = 1 minimized, dist, pred = bellman_ford_search(g, g.vertex(0), weights) and what I get is: File "/usr/lib/python2.7/dist-packages/graph_tool/search/__init__.py", line 1118, in bellman_ford_search zero, infinity)OverflowError: Python int too large to convert to C long. In case I add the infinity parameter, so minimized, dist, pred = bellman_ford_search(g, g.vertex(0), weights, infinity=int) I get File "graphTest2.py", line 26, in <module> minimized, dist, pred = bellman_ford_search(g, g.vertex(0), weights, infinity=int) File "/usr/lib/python2.7/dist-packages/graph_tool/search/__init__.py", line 1103, in bellman_ford_search infinity = _python_type(dist_map.value_type())(infinity)TypeError: descriptor '__trunc__' of 'int' object needs an argument and the same happens with infinity=float. I tested dijkstra_search, that uses infinity as well, but I don't get any problem. Could you please tell me if I am doing something wrong, or if there is a problem? Thanks and best regards,Alessandro

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Property maps: Type name: Safe to use "bool" type to store values between 1 and 100?
by Didier Guillevic 02 Dec '14

02 Dec '14

Hi, I want to add a ‘weight’ edge attribute with weights ranging from 1 to 100 (values that fit in an unsigned char). In order to save some space, I would like to store those weights in an uint8_t instead of int16_t. The uint8_t is accessible through the ‘bool’ type name for the Property Maps. - I checked that serializing and de-serializing ‘bool’ type names with values in the range [1-100] works fine. - I also checked that running PageRank using the ‘weight’ edge property gives the same result whether the weights ([1-100]) are stored as type ‘bool’ or type ‘int16_t’. My question is it safe to assume that it will always work. Do some of the algorithms check the type name of the property and seeing ‘bool’, those algorithms could decide to use true/false values rather than an integer in range [0-255]. Thanks for any feedback, Didier

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graph-tool December 2014