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

Efficient Bipartite Projection
by Carlos Andrade 17 Sep '15

17 Sep '15

Dear all, I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that). I started of from (1) Gephi plugin ( https://marketplace.gephi.org/plugin/multimode-networks-transformations-2/) which after running for a couple hours almost froze my computer and output no graph (I had to force quit it). My second attempt was (and is) on igraph ( http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection ) I came across this post: http://stackoverflow.com/questions/606516/python-graph-library And read about graph-tool and how efficient it is compared to the igraph and networkx (which I was about to try but given up when I saw the time table). Thank you for your attention,

5 8

graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> thanks - -- 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 12

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

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

efficiency of graph creation
by thekswenson 29 Apr '15

29 Apr '15

I've been using networkx to simply create a graph and check the connected components. The bottleneck of the operation is the creation of the edges. I've heard that graph-tool is very efficient so I've replaces the code with a graph-tool graph. To my surprise, the creation of a graph-tool graph is MUCH slower than that of a networkx graph. Am I doing something wrong? I've created a small sample program (at the bottom of this message) to test this speed... it creates a graph in a very natural way: pairs of objects that should be connected by an edge are iterated through. We happen to give every possible pair of objects in this example so the complete graph is created. Here is runsnake image of where the running-time is going: <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> The Code: #!/usr/bin/python """ Create graphs in networkx and graph-tool. """ import networkx as nx from graph_tool.all import * from itertools import combinations def graph_tool_create(): """ Create a graph_tool graph given a list of pairs. """ G = Graph(directed=False) objectset = set() for o1,o2 in get_pairs_of_objects(): if(o1 not in objectset): u = G.add_vertex() objectset.add(o1) if(o2 not in objectset): v = G.add_vertex() objectset.add(o2) G.add_edge(u,v) def nx_create(): """ Create a graph_tool graph given a list of pairs. """ G = nx.Graph() for o1,o2 in get_pairs_of_objects(): G.add_edge(o1,o2) def get_pairs_of_objects(): """ Generate pairs of objects. """ n = 5000 for a,b in combinations(range(n),2): yield a,b graph_tool_create() nx_create() -- 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 10

update graph draw in a thread
by Xun Xiao 29 Apr '15

29 Apr '15

I am currently trying to update the GraphWidget in a thread (because the topology, and plot properties change from time to time). I put regenerate_surface() and queue_draw() in the thread, however, the GraphWdiget will become dead.. Does anyone know a good way to update the drawing? thanks a lot! -- 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

Average calculation from vector<double> property
by desert_rain 28 Apr '15

28 Apr '15

Hi, I am using graph-tool for my research, thanks for creating graph-tool. I need to calculate average values from vertex and edge properties. Property types are "vector<double>". When I use the "edge_average" function, program gives 'RuntimeError'. How can I calculate averages from vector property? Example code below: g = Graph() v1 = g.add_vertex() v2 = g.add_vertex() v3 = g.add_vertex() e1 = g.add_edge(v1, v2) e2= g.add_edge(v2, v3) e3= g.add_edge(v1, v3) e_properties = g.new_edge_property("vector<double>") e_properties[e1] = [0.0005] e_properties[e2] = [0.006,0.0007] edge_average(g, e_properties) Thanks! -- 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

Compilation error in Debian 7
by Santiago Videla 23 Apr '15

23 Apr '15

Hi, I'm trying to compile from sources but I'm getting some errors. While "configure" went well on checking all dependecies, when I run make I got a bunch of errors compiling graph_blockmodel.lo (full traceback has 1.1MB, so I included only the end of it below) Any idea of what could be the issue? Does anyone compiled graph-tool on Debian 7? Regards, $ ./configure --enable-openmp checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for gcc option to accept ISO C99... unsupported checking for gcc option to accept ISO C89... (cached) none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking target system type... x86_64-unknown-linux-gnu checking whether to enable debug info...... no checking whether C++ compiler supports -std=gnu++11... yes checking whether to enable function inlining...... yes checking whether to enable optimizations...... yes checking whether to enable symbol visibility manipulation...... yes checking whether to enable parallel algorithms with openmp...... yes checking whether to enable cairo drawing...... yes checking for main in -lm... yes checking for main in -lbz2... no checking for main in -lexpat... yes ================ Detecting python ================ checking for a Python interpreter with version >= 2.6... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.3'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/dist-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes graph-tool will be installed at: /usr/lib/python2.7/dist-packages =========================== Using python version: 2.7.3 =========================== 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... yes 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... yes checking whether to cgal debbuging with valgrind...... no checking python module: numpy... yes checking for /usr/lib/pymodules/python2.7/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking /usr/lib/python2.7/dist-packages/scipy/weave/scxx/object.h usability... yes checking /usr/lib/python2.7/dist-packages/scipy/weave/scxx/object.h presence... yes checking for /usr/lib/python2.7/dist-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... yes checking CGAL/version.h presence... yes checking for CGAL/version.h... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... yes checking python module: cairo... yes checking pycairo/pycairo.h usability... yes checking pycairo/pycairo.h presence... yes checking for pycairo/pycairo.h... yes checking whether to enable sparsehash...... yes checking for SPARSEHASH... yes checking sparsehash/dense_hash_set usability... yes checking sparsehash/dense_hash_set presence... yes checking for sparsehash/dense_hash_set... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/graph/Makefile config.status: creating src/graph/centrality/Makefile config.status: creating src/graph/clustering/Makefile config.status: creating src/graph/community/Makefile config.status: creating src/graph/correlations/Makefile config.status: creating src/graph/draw/Makefile config.status: creating src/graph/flow/Makefile config.status: creating src/graph/generation/Makefile config.status: creating src/graph/layout/Makefile config.status: creating src/graph/search/Makefile config.status: creating src/graph/spectral/Makefile config.status: creating src/graph/stats/Makefile config.status: creating src/graph/topology/Makefile config.status: creating src/graph/util/Makefile config.status: creating src/graph_tool/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: Modifying libtool to correctly link libstdc++ before anything else... $ make .... .... .... Making all in community make[4]: Entering directory `/home/santiago/Downloads/graph-tool-2.2.42/src/graph/community' CXX graph_blockmodel.lo .... .... .... graph_blockmodel.cc:430:76: required from here graph_blockmodel.cc:336:105: error: no matching function for call to ‘graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>::ConstantPropertyMap(<brace-enclosed initializer list>)’ graph_blockmodel.cc:336:105: note: candidates are: In file included from ./../graph.hh:35:0, from ./../graph_filtering.hh:21, from graph_blockmodel.cc:28: ./../graph_properties.hh:606:5: note: graph_tool::ConstantPropertyMap<Value, Key>::ConstantPropertyMap() [with Value = std::array<int, 1ul>; Key = long unsigned int] ./../graph_properties.hh:606:5: note: candidate expects 0 arguments, 1 provided ./../graph_properties.hh:605:5: note: graph_tool::ConstantPropertyMap<Value, Key>::ConstantPropertyMap(const value_type&) [with Value = std::array<int, 1ul>; Key = long unsigned int; graph_tool::ConstantPropertyMap<Value, Key>::value_type = std::array<int, 1ul>] ./../graph_properties.hh:605:5: note: no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘const value_type& {aka const std::array<int, 1ul>&}’ ./../graph_properties.hh:596:7: note: constexpr graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>::ConstantPropertyMap(const graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>&) ./../graph_properties.hh:596:7: note: no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘const graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>&’ ./../graph_properties.hh:596:7: note: constexpr graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>::ConstantPropertyMap(graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>&&) ./../graph_properties.hh:596:7: note: no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘graph_tool::ConstantPropertyMap<std::array<int, 1ul>, long unsigned int>&&’ make[4]: *** [graph_blockmodel.lo] Error 1 make[4]: Leaving directory `/home/santiago/Downloads/graph-tool-2.2.42/src/graph/community' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/santiago/Downloads/graph-tool-2.2.42/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/santiago/Downloads/graph-tool-2.2.42/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/santiago/Downloads/graph-tool-2.2.42' make: *** [all] Error 2 -- Santiago Videla http://www.linkedin.com/in/svidela

1 1

MAKE failure in CentOS
by Jose Albornoz 22 Apr '15

22 Apr '15

Hi there. I am trying to install Graph-tool on a Linux server with CentOS 6.6, gcc 4.7.2, Boost 1.58.0. I am using this script to run the configure file: export BOOST_ROOT=$HOME/boost_1_58_0 export PKG_CONFIG_PATH=$HOME/cairomm-1.2.0/:$HOME/lib/pkgconfig ./configure --prefix=$HOME --with-sparsehash-prefix=google CPPFLAGS="- I$HOME/boost_1_58_0" LDLFLAGS="$HOME/boost_1_58_0" scl enable devtoolset-1.1 bash configure seems to go well without any abnormal message: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for gcc option to accept ISO C99... unsupported checking for gcc option to accept ISO C89... (cached) none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld checking if the linker (/opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /opt/centos/devtoolset-1.1/root/usr/bin/nm -B checking the name lister (/opt/centos/devtoolset-1.1/root/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1966080 checking how to convert x86_64-unknown-linux-gnu file names to x86_64- unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /opt/centos/devtoolset-1.1/root/usr/libexec/gcc/x86_64- redhat-linux/4.7.2/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /opt/centos/devtoolset-1.1/root/usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld -m elf_x86_64 checking if the linker (/opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/opt/centos/devtoolset- 1.1/root/usr/libexec/gcc/x86_64-redhat-linux/4.7.2/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking target system type... x86_64-unknown-linux-gnu checking whether to enable debug info...... no checking whether C++ compiler supports -std=gnu++11... yes checking whether to enable function inlining...... yes checking whether to enable optimizations...... yes checking whether to enable symbol visibility manipulation...... yes checking whether to enable parallel algorithms with openmp...... no checking whether to enable cairo drawing...... yes checking for main in -lm... yes checking for main in -lbz2... yes checking for main in -lexpat... yes ================ Detecting python ================ checking for a Python interpreter with version >= 2.6... python checking for python... /usr/local/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site- packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for python2.7... (cached) /usr/local/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.8'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/local/include/python2.7 checking for Python library path... -L/usr/local/lib -lpython2.7 checking for Python site-packages path... /usr/local/lib/python2.7/site- packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes graph-tool will be installed at: /usr/local/lib/python2.7/site-packages =========================== Using python version: 2.7.8 =========================== 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... yes 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... yes checking whether to cgal debbuging with valgrind...... no checking python module: numpy... yes checking for /usr/local/lib/python2.7/site- packages/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking /usr/local/lib/python2.7/site- packages/scipy/weave/scxx/object.h usability... yes checking /usr/local/lib/python2.7/site- packages/scipy/weave/scxx/object.h presence... yes checking for /usr/local/lib/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... yes checking CGAL/version.h presence... yes checking for CGAL/version.h... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... yes checking python module: cairo... no checking pycairo/pycairo.h usability... yes checking pycairo/pycairo.h presence... yes checking for pycairo/pycairo.h... yes checking whether to enable sparsehash...... yes checking for SPARSEHASH... yes checking google/dense_hash_set usability... yes checking google/dense_hash_set presence... yes checking for google/dense_hash_set... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/graph/Makefile config.status: creating src/graph/centrality/Makefile config.status: creating src/graph/clustering/Makefile config.status: creating src/graph/community/Makefile config.status: creating src/graph/correlations/Makefile config.status: creating src/graph/draw/Makefile config.status: creating src/graph/flow/Makefile config.status: creating src/graph/generation/Makefile config.status: creating src/graph/layout/Makefile config.status: creating src/graph/search/Makefile config.status: creating src/graph/spectral/Makefile config.status: creating src/graph/stats/Makefile config.status: creating src/graph/topology/Makefile config.status: creating src/graph/util/Makefile config.status: creating src/graph_tool/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: Modifying libtool to correctly link libstdc++ before anything else... However, when running MAKE I get the following: [jalbornoz@kopke graph-tool-2.2.42]$ make make all-recursive make[1]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42' Making all in src make[2]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src' Making all in graph make[3]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/gra ph' Making all in centrality make[4]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/gra ph/centrality' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/grap h/centrality' Making all in clustering make[4]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/gra ph/clustering' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/grap h/clustering' Making all in community make[4]: Entering directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/gra ph/community' CXX graph_blockmodel.lo cc1plus: error: unrecognized command line option "-std=gnu++11" cc1plus: warning: unrecognized command line option "-Wno-unused-local- typedefs" make[4]: *** [graph_blockmodel.lo] Error 1 make[4]: Leaving directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/grap h/community' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src/grap h' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/jalbornoz/downloads/graph-tool- 2.2.42/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/jalbornoz/downloads/graph-tool-2.2.42' make: *** [all] Error 2 Any hints on how to solve this issue are greatly appreciated Cheers

3 2

weird in deleting vertices and edges
by Bo Wu 21 Apr '15

21 Apr '15

Hi all, I found something weird in deleting vertices and edges of a graph. Say I simply create a graph like: g = Graph(directed=False) g.add_vertex(7) g.add_edge(g.vertex(0), g.vertex(1)) g.add_edge(g.vertex(1), g.vertex(2)) g.add_edge(g.vertex(2), g.vertex(3)) g.add_edge(g.vertex(3), g.vertex(4)) g.add_edge(g.vertex(2), g.vertex(5)) g.add_edge(g.vertex(5), g.vertex(6)) del_list = [g.vertex(1), g.vertex(3)] for v in reversed(sorted(del_list)): print 'deleting vertex', int(v) ## for ve in v.out_edges(): ## print 'deleting edges', ve.source(), ve.target() ## g.remove_edge(ve) g.remove_vertex(v, fast=True) The above code will delete vertex 3 first, then vertex 1 as expected. However, in order to keep correct topology, we should delete some related edges first, like the three commented lines (start with "##"). But if you uncomment the three lines, weird thing happens: the program will delete vertex 1 first, then vertex 3. Of course I can sort the vertex index instead of vertex descriptor to avoid the problem. But I am wondering where is wrong. Could anyone explain this? -- Cheers, Bo Wu

2 5