April 2015 - graph-tool - archives.skewed.de

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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mayavi with graph-tool
by Bo Wu 20 Apr '15

20 Apr '15

Hello all, I am pretty new to graph-tool and trying it because of the fast speed. However, it seems that graph-tool cannot work together with mlab in mayavi. I am basically planning to plot a 3D graph using mlab. But when I import mlab from mayavi, the program always prints the following warning and then becomes frozen. I don't know why. Is it the problem of gtk? I just want to use graph-tool data structure and algorithms output : /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: cannot register existing type `GtkWidget' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: cannot add class private field to invalid type '<invalid>' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: g_type_add_interface_static: assertion `G_TYPE_IS_INSTANTIATABLE (instance_type)' failed g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: cannot register existing type `GtkBuildable' g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: g_type_interface_add_prerequisite: assertion `G_TYPE_IS_INTERFACE (interface_type)' failed g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:142: Warning: g_once_init_leave: assertion `result != 0' failed g_type = info.get_g_type() /usr/lib/python2.7/dist-packages/gi/module.py:146: Warning: g_type_get_qdata: assertion `node != NULL' failed type_ = g_type.pytype -- Cheers, Bo Wu

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Multi-Objective A-star + Vector Weight + Non-dominated Distances
by haitam 17 Apr '15

17 Apr '15

Hi All, I would like to know whether with the actual A-star, we can be able to develop a multi-objective approach. After a brief introduction I came to know that it is possible to have a vector weight, and customize the different steps of the algorithm with a Visitor. Now I am wondering if: + the objective function (distance) can only be a scalar and not a vector ? + Is the algorithm (behind the scenes) bear a multi-objective implementation, for instance for A* a tree is constructed, but for MOA* rather an Acyclic Graph is constructed. If not supported, I should maybe be add a new search algorithm to the set. What is the best way to extend Graph Tool ? Do I have only to create the graph_moastar.cc, graph_moastar.hh, graph_moastar.lo and update the Makefile in the src/graph/search folder ? Thank you for your attention, ;) -- 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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unable to load pgp.xml
by 俊赵 13 Apr '15

13 Apr '15

hi all, i am new to graph tool, and i encounter a problem i got the performance test files from http://graph-tool.skewed.de/performance when i run gt_bench.py, it shows [zhaojun@fedora performance]$ python gt_bench.py Traceback (most recent call last): File "gt_bench.py", line 6, in <module> g = load_graph("pgp.xml") File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line 2352, in load_graph g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp) File "/usr/lib/python2.7/site-packages/graph_tool/__init__.py", line 1989, in load ignore_ep, ignore_gp)IOError: error reading from file 'pgp.xml':parse error: on line 1, column 0: not well-formed (invalid token) i have no idea whether it is something related with the formate of xml file or with the graph tool API i installed thanks Zhao Jun

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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.

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