June 2019 - graph-tool - archives.skewed.de

Ubuntu Disco
by Spam Spam 17 Jun '19

17 Jun '19

3 11

[SBM on Dense Graphs]
by Jean Christophe Cazes 14 Jun '19

14 Jun '19

Hello, I intend to use graph_tool for a big network, +100k nodes and very dense. The dataset i'm working with at the moment is ~ 40/50 GB csv containing vertices and edges as transactions. Is it realistic to try SBM on such graph both computationnally and would this be theoretically useful? If it isnt computationnally, how big can my subgraph be in order to be feasible? Note: I will rent a Google Cloud Platform VM to do so. Thank you

4 6

problem when installing: libxml2.la: No such file or directory
by Angeles rodriguez de cara 13 Jun '19

13 Jun '19

Dear all, I am trying to install graph tools from source as I cannot install it using brew. I'm on a linux mint 19 box. I include below the output of ./configure and I attach the config.log. Many thanks! checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu 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 how to create a pax tar archive... gnutar 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 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-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-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 for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking whether g++ supports C++14 features by default... yes checking whether to enable debug info... no checking whether to enable parallel algorithms with openmp... checking for OpenMP flag of C++ compiler... -fopenmp checking whether to enable cairo drawing... yes checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes checking for a Python interpreter with version >= 2.7... python checking for python... /home/angeles/anaconda3/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/angeles/anaconda3/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.16'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/angeles/anaconda3/include/python2.7 checking for Python library path... -L/home/angeles/anaconda3/lib -lpython2.7 checking for Python site-packages path... /home/angeles/anaconda3/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 checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::Python library is available... yes checking whether boost_python is the correct library... 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::Context library is available... yes checking for exit in -lboost_context... yes checking whether the Boost::Coroutine library is available... yes checking for exit in -lboost_coroutine... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for __gmpz_init in -lgmp... yes checking for __gmpz_init in -lgmp... (cached) yes checking whether CGAL is available in /usr... yes checking whether to enable cgal debbuging with valgrind... no checking python module: numpy... yes checking for numpy/arrayobject.h... 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... no not found by pkgconfig, trying default... checking sparsehash/dense_hash_set usability... yes checking sparsehash/dense_hash_set presence... yes checking for sparsehash/dense_hash_set... yes configure: pkgconfig directory is ${libdir}/pkgconfig checking our pkgconfig libname... graph-tool-py2.7 checking our pkgconfig version... 2.27 checking our pkgconfig_libdir... ${libdir}/pkgconfig expanded our pkgconfig_libdir... /usr/local/lib/pkgconfig checking our pkgconfig_libfile... graph-tool-py2.7.pc checking our package / suffix... graph-tool / checking our pkgconfig description... graph-tool Python library checking our pkgconfig requires... checking our pkgconfig ext libs... -L/home/angeles/anaconda3/lib -lpython2.7 -lboost_python checking our pkgconfig cppflags... -I/home/angeles/anaconda3/lib/python2.7/site-packages/graph_tool/include -I/home/angeles/anaconda3/lib/python2.7/site-packages/graph_tool/include/boost-workaround -I/home/angeles/anaconda3/include/python2.7 -pthread -I/usr/include -I/home/angeles/anaconda3/lib/python2.7/site-packages/numpy/core/include checking our pkgconfig ldflags... noninstalled pkgconfig -L /home/angeles/Downloads/graph-tool-2.27/src/.libs noninstalled pkgconfig -I /home/angeles/Downloads/graph-tool-2.27/. 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/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/inference/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 config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtoo l commands config.status: executing graph-tool-py2.7.pc commands config.status: creating graph-tool-py2.7.pc.in config.status: creating graph-tool-py2.7.pc config.status: creating graph-tool-py2.7-uninstalled.pc config.status: creating graph-tool-py2.7-uninstalled.sh ================================================================================ESC(BESC[m ESC[32m CONFIGURATION SUMMARY ESC(BESC[m ESC[32m================================================================================ESC(BESC[m Using python version: 2.7.16 Python interpreter: /home/angeles/anaconda3/bin/python Installation path: /home/angeles/anaconda3/lib/python2.7/site-packages/graph_tool C++ compiler (CXX): g++ C++ compiler version: 7 Prefix: /usr/local Pkgconfigdir: ${libdir}/pkgconfig Python CPP flags: -I/home/angeles/anaconda3/include/python2.7 Python LD flags: -L/home/angeles/anaconda3/lib -lpython2.7 Boost CPP flags: -pthread -I/usr/include Boost LD flags: -lboost_iostreams -lboost_python -lboost_regex -lboost_context -lboost_coroutine Numpy CPP flags: -I/home/angeles/anaconda3/lib/python2.7/site-packages/numpy/core/include Sparsehash CPP flags: CGAL CPP flags: -I/usr/include CGAL LD flags: -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread Expat CPP flags: -I/usr/include Expat LD flags: -L/usr/lib -lexpat Cairomm CPP flags: -I/usr/include/cairomm-1.0 -I/usr/lib/x86_64-linux-gnu/cairomm-1.0/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/sigc++-2.0 -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include Cairomm LD flags: -lcairomm-1.0 -lcairo -lsigc-2.0 OpenMP compiler flags: -fopenmp OpenMP LD flags: Extra CPPFLAGS: -DNDEBUG Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 Extra LDFLAGS: Using OpenMP: yes Using sparsehash: yes Using cairo: yes ================================================================================

2 1

Installing graph-tool
by roaasoloh 11 Jun '19

11 Jun '19

I'm on Ubuntu 18.04 and trying to install this to use in anaconda Pycharm editor, following the instructions mentioned for ubuntu here https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#nat… trying the three DISTRIBUTION none is working,and trying to verify the package using both keys, whether the mentioned in the link or that one in the mailing list: 612DEFB798507F25 or 7A80C8ED4FCCBE09 it gives: gpg: keyserver receive failed: No keyserver available and definitely the result of apt-get install ... is : E: Unable to locate package python3-graph-tool -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

1 0

About Vertex
by JeanPierre Paillet 03 Jun '19

03 Jun '19

Hello: Given a Vertex descriptor, I can ask whether it is valid. But I can't find a way to get the graph to which it belongs. I was sure I had seen 'v.graph()' somewhere, but it must have been in a dream 🙂

2 1