graph-tool February 2014

graph-tool@skewed.de

10 participants
18 discussions

Graphviz layout issue - neato >2000 vertices
by CitSci 26 Feb '14

26 Feb '14

Hi, I am trying to do a layout of a 2,000 vertex graph with Graphviz and neato in Linux. This graph is a minimum spanning tree (MST) created from the topology module using integer edge weights for layout. I have not selected any options about edge length, etc. only specified 'neato' with png output. However, the output is an extremely bunch group of nodes in a circular region with no resolution of the edges. I am wondering if this is a GraphViz plotting issue or if this is a issue with the MST? Any help 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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Strange bug on install
by CFK 21 Feb '14

21 Feb '14

Hi all, I just installed graph-tool on my work machine which is running OS X 10.8.5. I installed it via macports via 'port install py33-graph-tool'. When I try to import graph tool, I get the following: >>> from graph_tool.all import * dyld: lazy symbol binding failed: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace dyld: Symbol not found: __ZN5boost6python7objects23register_dynamic_id_auxENS0_9type_infoEPFNSt3__14pairIPvS2_EES5_E Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace Trace/BPT trap: 5 Which crashes python and results in my being back at a regular terminal prompt. Has anyone else seen this? Any ideas how to fix it? Thanks, Cem Karan

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Removed edges in EdgePropertyMap
by Guillaume Gay 21 Feb '14

21 Feb '14

Hi Tiago, hi all, When an edge is removed from a graph, it still occupies a place in the graphs EdgePropertyMap, leading to the following being |False|: |edge_prop.a.shape[0] == graph.num_edges()| Is there a way to circumvent this? Best, Guillaume

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make duration of graph-tool
by Stefan Klingelschmitt 21 Feb '14

21 Feb '14

Hey, I'm trying to install graph-tool on my OpenSuse 12.2. The Configuration seems to have worked, after installing all the dependencies. Unfornutately the compiling seems to take hours. Yesterday I let it run for about 6 hours and it has not finished. It seems like the compiling of the individual functions takes up a lot of time, for example: ... Making all in centrality make[4]: Entering directory `/home/sklingel/bin/PyAdditionalPackages/graph-tool-2.2.27/src/graph/centrality' CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo ... the graph_pagerank.lo has needed round about two hours to compile.... I assume this isn't a normal behavior? Thanks

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virtual memory exhausted ...can not allocate memory
by NemiRathore 19 Feb '14

19 Feb '14

I am having Intel i7 processor with 4GB Ram. After issuing make command I am getting following set of messages;To resolve this problem I created an additional swap space of 2GB and then reissue the 'make' command but still got same set error messages; ----------------------------------------------------------------------------------------------------------------------------------------------------------- make all-recursive make[1]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1' Making all in src make[2]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1/src' Making all in graph make[3]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph' Making all in centrality make[4]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/centrality' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/centrality' Making all in clustering make[4]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/clustering' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/clustering' Making all in community make[4]: Entering directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/community' CXX graph_community_network_eavg_imp1.lo ^[[Dvirtual memory exhausted: Cannot allocate memory make[4]: *** [graph_community_network_eavg_imp1.lo] Error 1 make[4]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph/community' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/ncrathore/graph-tool-2.2.29.1' make: *** [all] Error ----------------------------------------------------------------------------------------------------------------------------- Please somebody help me to sort out this problem -- 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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Ubuntu 13.10 cannot configure properly
by Liu 18 Feb '14

18 Feb '14

Hi,everyone I have some problems with installing graph-tools. After I execure ./configure graph-tools, it stops with a message saying libstdc++ config.status: executing libtool commands configure: Modifying libtool to correctly link libstdc++ before anything else...I am not fimiliar with Linux...so I don't know how I can I link my libstd to libtool. I install boost-1.55.0 ipython-dev, python with spyder, scipy, numpy, expat, cgal and sparsehash. My OS is Ubuntu 13.10 64bit with gnome 3.10. The Internet access is not good. So I cannot use the sources that you provide. thx for help, Liu -- 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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Installing graph-tool in sagemath
by Juan I. Perotti 12 Feb '14

12 Feb '14

Hello, I am trying to install graph-tool in sagemath ( check http://www.sagemath.org/ <http://www.sagemath.org/> ), under Ubuntu 12.04. Basically, sagemath is python with many good modules helpful for mathematics, and why not physics. sagemath has its own built version of python, which is standard by using a virtual environment. The idea is, I guess, not to mess up with your system python. By typing in a terminal $ sage -sh you enter into sagemath virtual environment, which looks like: (sage -sh) $ therefore, if you try to run a python console by typing (sage -sh)$ python then, it will run the python built in sage's virtual environment. >From the virtual environment I have installed CGAL, and then, I tried to configure graph-tool typing: (sage -sh) graph-tool-2.2.29$ ./configure 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... cpp 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 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... ld checking if the linker (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 whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes 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 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 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 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 (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++... ld -m elf_x86_64 checking if the linker (ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (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 (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 graph filtering...... yes checking whether to enable parallel algorithms with openmp...... no checking whether to enable cairo drawing...... yes checking whether to enable sparsehash...... 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... /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/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) /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.5'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/include/python2.7 checking for Python library path... -L/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.12/local/lib -lpython2.7 checking for Python site-packages path... /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes graph-tool will be installed at: /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages =========================== Using python version: 2.7.5 =========================== checking for boostlib >= 1.38.0... 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 /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/scipy/weave/scxx/object.h usability... yes checking /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/scipy/weave/scxx/object.h presence... yes checking for /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/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... no checking CGAL/version.h presence... no checking for CGAL/version.h... no configure: error: CGAL headers not found As you can see, the config is using sage's version of python. However, it does not find CGAL's headers. Do you know why? Best Regards, Juan -- 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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Installation of Graph-tool in windows 7
by vrohani 03 Feb '14

03 Feb '14

Dear friends, I am quite new in Graph-tool. would you please help me to install it in windows 7? Is it possible? Thank you -- 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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graph-tool February 2014