graph-tool May 2015

graph-tool@skewed.de

14 participants
27 discussions

Porting to Windows
by Fabrice Popineau 07 May '15

07 May '15

Hi, I don't know if it is right to pollute this list with my problems in trying to compile graph-tool for Win64. I'll try to make it brief. Using MSYS2/MinGW64, I managed to compile the whole src/graph modules and install them as *.pyd modules in the site-packages/graph_tool directory, along with the Python files. Unfortunately, I get a segfault when importing graph_tool.libgraph_tool_core . The segfault happens deep in libboost_python3. Before posting a long backtrace, maybe someone may offer some clue on what is happening. I have posted some details about what I did below. If someone is interested and/or has ideas on how o go on, I'll be glad to share and work on this problem. (And I must say that I would love to get this tool to work under Windows, because it seems to be one of the best of its kind!) Best regards, Fabrice The background is: python 3.4, boost 1.57, clang 3.5.1 (g++ 4.9.2 as provided with mingw64 couldn't compile a few objects without segfaulting). Is it possible that there is a conflict among those libs/tools (of thread model for example)? Currently I have configured like this: ./configure --enable-debug --disable-optimize CFLAGS="-I/mingw64/include" LDFLAGS="-L/mingw64/lib" CC=clang CXX='clang -std=c++11 -m64 -DMS_WIN64=1' CXXCPP='clang -E -std=c++11 -m64 -DMS_WIN64=1' PYTHON=python3 Then I run 'make -k -j 8' to compile all the objects. Linking the various dlls fails, because under Windows, you can't link graph_tool_centrality.dll without referencing grap_tool_core.dll.a. However the build process is not prepared to do that and in the right order. So I manually replicated what libtool does, ie : clang -std=c++11 -shared -nostdlib C:/Local/MSys64/mingw64/x86_64-w64- mingw32/lib/dllcrt2.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtbegin.o .libs/*.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtend.o - L/mingw64/lib -O3 - Wl,--export-all-symbols -Wl,--as-needed -o .libs/libgraph_tool_core.dll -Wl,-- enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libgraph_tool_core.dll.a -lpython3.4m -lboost_iostreams -lboost_python3 - lboost_regex -lboost_system -lCGAL -lgmp -lcairomm-1.0 -lcairo -lexpat -lbz2 - lstdc++ -lpthread -lgcc_s -lgcc -lmoldname -lmingwex -lmingw32 -lmsvcrt - ladvapi32 -lshell32 -luser32 -lkernel32 for s in ${subdirs}; do (cd $s ; clang -std=c++11 -shared -nostdlib C:/Local/MSys64/mingw64/x86_64-w64- mingw32/lib/dllcrt2.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtbegin.o .libs/*.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtend.o ../.libs/libgraph_tool_core.dll.a -L/mingw64/lib -O3 -Wl,--export-all- symbols -Wl,--as-needed -o .libs/libgraph_tool_$s.dll -Wl,--enable-auto-image- base -Xlinker --out-implib -Xlinker .libs/libgraph_tool_$s.dll.a -lpython3.4m - lboost_iostreams -lboost_python3 -lboost_regex -lboost_system -lCGAL -lgmp - lcairomm-1.0 -lcairo -lexpat -lbz2 -lstdc++ -lpthread -lgcc_s -lgcc -lmoldname -lmingwex -lmingw32 -lmsvcrt -ladvapi32 -lshell32 -luser32 -lkernel32) done for i in `find . -name \*.dll` ; do cp $i /mingw64/lib/python3.4/site- packages/graph_tool/`basename $i .dll`.pyd; done At this point, the modules are installed. The only thing to change on the Python side is to remove the calls to getdlopenflags() and setdlopenflags() which are not available to Windows.

2 4

Remove an edge with a property
by William Stevenson 07 May '15

07 May '15

Hi, I have tried various methods and now it's time to ask for help. I am trying to simulate a distributed algorithm called H-graph, in this we start with a regular undirected graph with 3 vertices and constant degree d, say 8. We label these edges so we have d/2 Hamiltionian cycles please see [1] for an image. I have tried various methods to identify and remove an exact edge with a certain property value. I am using internal property maps, but all have failed. For reference I have tried find_edge and GraphView to isolate the edges with the required property, and you can find my current, broken code at [2]. The methods in question are set_nbr_pred/succ, and they are quite warped now from multiple failed attempts. Thanks in advance, William Stevenson [1] http://i.imgur.com/m2apKZ7.png [2] http://yhvh.co.uk/root/final-project/blob/nozmq/program/HgraphVertex.py

2 1

random_graph function crashes python
by ob 07 May '15

07 May '15

I am using random_graph() to generate graphs for given marginals. This seems to work well if the method does not need to create too many parallel edges. However, as soon as the marginals are significantly larger then the number of vertices the function tends to crash/hang up python. Here is a small example: >>> import graph_tool.all as gt >>> in_degr =[50,40,3] >>> out_degr=[40,3,50] >>> g = gt.random_graph(3, lambda i: (in_degr[i],out_degr[i]), >>> directed=True,parallel_edges=True) I tried this on OS X and Linux with similar results. I'm not sure I have the right approach here. I'd rather prefer to have weighted edges created then parallel edges. But I couldn't figure out how to do that. I have two questions: 1. Can anyone reproduce / solve the issue above? 2. Is there a way to generate directed graphs from marginals with weighted edges? Thanks, Olaf -- 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

Visualise categorical attributes read from graphml files (beginner)
by marten 05 May '15

05 May '15

Hi Tiago, I am trying to visualise a bipartite network (graphml, created with networkx), where node types are represented by vertex shape and other vertex attributes such as party affiliation by vertex colour and/or size. I would be very grateful for a code sample which could help illustrate how such non-computed attributes are retrieved from loaded graphml file and assigned to the graph. I was not able to figure this out reading through the documentation. Many thanks, Marten -- 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

install graph tool in Mac OS X 10.10
by 俊赵 05 May '15

05 May '15

hi all, i install graph tool in OS X 10.10 using command "sudo port install py-graph-tool" and i succeed but when i use graph tool, i must use python under root mode; how can i excute the python code under normal account mode without root privilege? also, when i use "from graph_tool.all improt *", i get "cannot import GTK+ module" error, but nevermind, it can still draw graph picture using other modules. thanks Zhao Jun

1 1

Mutliple destination Shortest Path Dijkstra
by François 04 May '15

04 May '15

Hello, I would like to implement a Mutliple destination Shortest Path Dijkstra, as in pgrouting <http://docs.pgrouting.org/dev/src/kdijkstra/doc/index.html> (see also this oldish networkx ticket <https://networkx.lanl.gov/trac/changeset/c1dbf20b5cbf2d15e1c08846b736572c32…> ). As I need it to be fast, I plan to do it in the CPP side of graph-tool. However, my CPP skills are quite limited. Would you have some references to guide me in the right direction ? Best, François -- 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 20

Porting to Windows
by Fabrice Popineau 02 May '15

02 May '15

Hi, I don't know if it is right to pollute this list with my problems in trying to compile graph-tool for Win64. I'll try to make it brief. Using MSYS2/MinGW64, I managed to compile the whole src/graph modules and install them as *.pyd modules in the site-packages/graph_tool directory, along with the Python files. Unfortunately, I get a segfault when importing graph_tool.libgraph_tool_core . The segfault happens deep in libboost_python3. Before posting a long backtrace, maybe someone may offer some clue on what is happening. I have posted some details about what I did below. If someone is interested and/or has ideas on how o go on, I'll be glad to share and work on this problem. (And I must say that I would love to get this tool to work under Windows, because it seems to be one of the best of its kind!) Best regards, Fabrice The background is: python 3.4, boost 1.57, clang 3.5.1 (g++ 4.9.2 as provided with mingw64 couldn't compile a few objects witout segfaulting). It is possible that there is a conflict among those libs/tools (of thread model for example). Currently I have configured like this: ./configure --enable-debug --disable-optimize CFLAGS="-I/mingw64/include" LDFLAGS="-L/mingw64/lib" CC=clang CXX='clang -std=c++11 -m64 -DMS_WIN64=1' CXXCPP='clang -E -std=c++11 -m64 -DMS_WIN64=1' PYTHON=python3 Then I run 'make -k -j 8' to compile all the objects. Linking the various dlls fails, because under Windows, you can't link graph_tool_centrality.dll without referencing grap_tool_core.dll.a. However the build process is not prepared to do that and in the right order. So I manually replicated what libtool does, ie : clang -std=c++11 -shared -nostdlib C:/Local/MSys64/mingw64/x86_64-w64- mingw32/lib/dllcrt2.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtbegin.o .libs/graph.o .libs/graph_exceptions.o .libs/graph_bind.o .libs/graph_copy.o .libs/graph_filtering.o .libs/graph_io.o .libs/graph_openmp.o .libs/graph_properties.o .libs/graph_properties_imp1.o .libs/graph_properties_imp2.o .libs/graph_properties_copy.o .libs/graph_properties_group.o .libs/graph_properties_ungroup.o .libs/graph_python_interface.o .libs/graph_python_interface_export.o .libs/graph_selectors.o .libs/graphml.o .libs/random.o .libs/read_graphviz_new.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtend.o -L/mingw64/lib -O3 - Wl,--export-all-symbols -Wl,--as-needed -o .libs/libgraph_tool_core.dll -Wl,-- enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libgraph_tool_core.dll.a -lpython3.4m -lboost_iostreams -lboost_python3 - lboost_regex -lboost_system -lCGAL -lgmp -lcairomm-1.0 -lcairo -lexpat -lbz2 - lstdc++ -lpthread -lgcc_s -lgcc -lmoldname -lmingwex -lmingw32 -lmsvcrt - ladvapi32 -lshell32 -luser32 -lkernel32 for s in ${subdirs}; do (cd $s ; clang -std=c++11 -shared -nostdlib C:/Local/MSys64/mingw64/x86_64-w64- mingw32/lib/dllcrt2.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtbegin.o .libs/*.o C:/Local/MSys64/mingw64/x86_64-w64-mingw32/lib/crtend.o ../.libs/libgraph_tool_core.dll.a -L/mingw64/lib -O3 -Wl,--export-all- symbols -Wl,--as-needed -o .libs/libgraph_tool_$s.dll -Wl,--enable-auto-image- base -Xlinker --out-implib -Xlinker .libs/libgraph_tool_$s.dll.a -lpython3.4m - lboost_iostreams -lboost_python3 -lboost_regex -lboost_system -lCGAL -lgmp - lcairomm-1.0 -lcairo -lexpat -lbz2 -lstdc++ -lpthread -lgcc_s -lgcc -lmoldname -lmingwex -lmingw32 -lmsvcrt -ladvapi32 -lshell32 -luser32 -lkernel32) done for i in `find . -name \*.dll` ; do cp $i /mingw64/lib/python3.4/site- packages/graph_tool/`basename $i .dll`.pyd; done At this point, the modules are installed. The only thing to change on the Python side is to remove the calls to getdlopenflags() and setdlopenflags() which are not available to Windows.

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graph-tool May 2015