graph-tool January 2015

graph-tool@skewed.de

12 participants
27 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

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

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

python3 version missing for 14.10 utopic
by offbyone 31 Jan '15

31 Jan '15

I see that there have been problems compiling for python3 in the past, so perhaps this is nothing more than that. I don't see python3-graph-tool, although the python version is present. Is python3 on it's way? Thanks for such a great (and fun) tool! -- 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

segmentation fault in PyInit_libgraph_tool_generation () at graph_generation.cc:99
by graph-tool＠v6y.net 30 Jan '15

30 Jan '15

Hi, using the latest git (or the release version), I get a segfault: $/usr/bin/python3.3 -c 'import graph_tool.all as gt' ; tail -n 1 /var/log/messages Segmentation fault Jan 19 04:42:12 localhost kernel: [196711.282646] python3.3[18903]: segfault at 16ae16 ip 000000000016ae16 sp 00007ffff2286a18 error 14 in libgmp.so.10.1.3[7f05c5edb000+78000] The end of the backtrace says: Program received signal SIGSEGV, Segmentation fault. 0x00000000011ab766 in ?? () #0 0x00000000011ab766 in ?? () #1 0x00007fffc3ddc357 in PyInit_libgraph_tool_generation () at graph_generation.cc:99 #2 0x00007ffff7a50afc in _PyImport_LoadDynamicModule (name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so', fp=0x0) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/importdl.c:86 #3 0x00007ffff7a50564 in imp_load_dynamic (self=<module at remote 0x7ffff7f40b90>, args=('graph_tool.generation.libgraph_tool_generation', '/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so')) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/import.c:1801 #4 0x00007ffff7976f07 in PyCFunction_Call (func=<built-in method load_dynamic of module object at remote 0x7ffff7f40b90>, arg=('graph_tool.generation.libgraph_tool_generation', '/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so'), kw={}) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/methodobject.c:81 Full backtraces and system information @ https://bugs.gentoo.org/show_bug.cgi?id=537042 line 99 of: https://github.com/count0/graph-tool/blob/master/src/graph/generation/graph… seems to be the fault location Any idea on what I should try to further isloate this? using: gcc 4.8.3 boost-1.56.0-r1 gmp-5.1.3-r1 Thanks! -Justin

2 15

subgraph_isomorphism (getting values)
by malwanain 29 Jan '15

29 Jan '15

I'me using subgraph isomorphism which comparing two graphs and the result is as follows: >>> print(subgraph_isomorphism(a, b)) [<PropertyMap object with key type 'Vertex' and value type 'int32_t', for Graph 0x10f52ff10, at 0x11e6eedd0, with values: [ 0 1 2 3 4 6 7 8 9 10 5]>, <PropertyMap object with key type 'Vertex' and value type 'int32_t', for Graph 0x10f52ff10, at 0x11e6eea10, with values: [ 0 1 2 3 4 6 7 8 9 10 11]>] My question is that is there any way to get full information about these numbers?(Vertex name or something)? regards -- 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 use vertex_text, etc when using g.save
by Andrew Terhune 28 Jan '15

28 Jan '15

Hello, I am brand new to graph-tool and found out with example how to label vertices when using graph_draw, as seen below graph_draw(g, vertex_text=labelv, edge_font_size=40, edge_text_distance=20, edge_marker_size=40, output="output.png") but do not see how to label vertices and edges when doing something like: g.save('testoutput.graphml','graphml') Can anyone assist with how this is done? Thanks!

2 1

graph isomorphic
by malwanain 27 Jan '15

27 Jan '15

Hi I've two graphs (.dot files) and I need to check if they are isomorphic or not. Do you have an example explaining how to load these files and check them in graph-tool? Regards -- 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

problem in import graph-tool
by malwanain 24 Jan '15

24 Jan '15

Hi I've installed graph-tool and when I try to import it, I get the following message: >>> import graph_tool Traceback (most recent call last): File "<stdin>", line 1, in <module> File "graph_tool/__init__.py", line 101, in <module> dl_import("from . import libgraph_tool_core as libcore") File "graph_tool/dl_import.py", line 57, in dl_import exec(import_expr, local_dict, global_dict) File "<string>", line 1, in <module> ImportError: cannot import name libgraph_tool_core Any one can help to solve this problem? Cheers! M -- 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 10

A paper using graph-tool published in Nature!
by Guillaume Gay 22 Jan '15

22 Jan '15

Hi every one, I've been working for some time now with the graph-tool library as a basis for the simulation of cellular tissue (aka epithelium), and this work has finally been published in the review Nature. As the library was instrumental in having the model up and running quickly, I thought I'd outline it here: Here is the paper itself: http://dx.doi.org/10.1038/nature14152 And a short blog post explaining the biology: http://damcb.com/paper_out.html Tiago, thanks a lot for your work! Best, Guillaume

2 1

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graph-tool January 2015