graph-tool February 2012

graph-tool@skewed.de

4 participants
5 discussions

Segmentation fault using shortest_distance
by Juan Manuel Tirado 20 Mar '16

20 Mar '16

Hi Tiago, I am trying to calculate the shortest distances of a graph after applying a filter. I have a code that looks like this: g=gt.load_graph("myGraph.xml",format="xml") #for later use distances = gt.shortest_distance(g) #extract the components of the graph comp = g.label_components(g) #This splits the graph in several components #I want to calculate the shortest distances #for the component 2 for example filtering = g.new_vertex_property("boolean") for v in g.vertices(): if comp[v]==2: filtering[v]=True else: filtering[v]=False #set the vertex filter g.set_vertex_filter(filtering) distances_comp=gt.shortest_distance(g) The last line of code rises a segmentation fault. I have plotted the graph with the filtered graph and its correct, also I can calculate the local_clustering_coefficient without problems. Am I doing something wrong? Is there any other way to filter the graph and calculate the shortest distances? Is this a bug? Thanks so much, Juan

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Parallel Processing
by Derek Ditch 21 Nov '13

21 Nov '13

I want to use graph-tool using the multiprocessing library in Python 2.6. I keep running into issues though with trying to share a full graph object. I can store the graph in a multiprocessing.Namespace, but it doesn't keep the dicts of properties. Example: def initNS( ns ): _g = Graph( directed = False) ns.graph = _g ns.edge_properties = { 'genres': _g.new_edge_property("vector<string>"), 'movieid': _g.new_edge_property("int"), } ns.vertex_properties = { 'personid': _g.new_vertex_property("int32_t") } """ Build property maps for edges and vertices to hold our data The graph vertices represent actors whereas movies represent edges """ # Edges _g.edge_properties["genres"] = ns.edge_properties['genres'] _g.edge_properties["movieid"] = ns.edge_properties['movieid'] # Vertices _g.vertex_properties["personid"] = ns.vertex_properties['personid'] ns.graph = _g ########## This initializes 'ns', which is a multiprocessing.Namespace. The problem is that for example, ns.edge_properties[ * ] tells me that the type isn't pickle-able. I tried to just skip that and use the _g.edge_properties to access it, but those dicts aren't carried over to the different process in the pool. Presumably b/c they aren't pickle-able. Any thoughts about how to fix this? (For those interested, I'm attempting to use the IMDbPy library to do some graph analysis on the relationships among actors and movies. Each process has it's own db connection and trying to populate the graph with actor and movie information in parallel since it's a pretty large and dense graph. Somewhere in the neighborhood of 250,000+ vertices for just a depth of three relationships) Thanks, -- Derek

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ImportError: No module named graph_tool.all
by Oscar Vargas Torres 23 Feb '12

23 Feb '12

Hi Tiago! $ $PYTHON_VERSION bash: 2.7: command not found $ uname -a Linux compu4 3.2.6-2-ARCH #1 SMP PREEMPT Thu Feb 16 10:10:02 CET 2012 x86_64 AMD Phenom(tm) II X6 1055T Processor AuthenticAMD GNU/Linux $ pacman -Q boost boost 1.48.0-2 $ pacman -Q boost-libs boost-libs 1.48.0-2 $ pacman -Q python2 python2 2.7.2-5 $ pacman -Q autoconf autoconf 2.68-2 $ pacman -Q automake automake 1.11.3-1 $ pacman -Q libtool libtool 2.4.2-3 $ pacman -Q gcc gcc 4.6.2-7 $ pacman -Q openmpi openmpi 1.5.4-4 $ pacman -Q expat expat 2.0.1-7 $ pacman -Q python2-numpy python2-numpy 1.6.1-1 $ pacman -Q python2-scipy python2-scipy 0.10.0-1 $ pacman -Q cgal cgal 3.9-4 $ pacman -Q graphviz graphviz 2.28.0-8 $ git clone git://git.skewed.de/graph-tool $ cd graph-tool $ autoreconf -f -i configure.ac:34: warning: AC_ARG_PROGRAM was called before AC_CANONICAL_TARGET ../../lib/autoconf/general.m4:1834: AC_CANONICAL_TARGET is expanded from... configure.ac:34: the top level configure.ac:34: warning: AC_ARG_PROGRAM was called before AC_CANONICAL_TARGET ../../lib/autoconf/general.m4:1834: AC_CANONICAL_TARGET is expanded from... configure.ac:34: the top level libtoolize: putting auxiliary files in `.'. libtoolize: copying file `./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:34: warning: AC_ARG_PROGRAM was called before AC_CANONICAL_TARGET ../../lib/autoconf/general.m4:1834: AC_CANONICAL_TARGET is expanded from... configure.ac:34: the top level configure.ac:34: warning: AC_ARG_PROGRAM was called before AC_CANONICAL_TARGET ../../lib/autoconf/general.m4:1834: AC_CANONICAL_TARGET is expanded from... configure.ac:34: the top level configure.ac:163: error: possibly undefined macro: AC_PYTHON_DEVEL If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. configure.ac:202: error: possibly undefined macro: AC_PYTHON_MODULE autoreconf: /usr/bin/autoconf failed with exit status: 1 Then I added at the beginning of Makefile.am: ACLOCAL_AMFLAGS = -I m4 after $ autoreconf -f -i I can do $ ./configure --enable-openmpi $ make -j3 After a while (I have 6 cores on my processor and I had to use 3 cores because of the RAM requirements... I got 8 GB of RAM), I can install with $ sudo make install But when in the ipython2 prompt I get the following error: In [2]: from graph_tool.all import * --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /home/oscar/graph-tool/<ipython-input-2-100bbe2bc9d9> in <module>() ----> 1 from graph_tool.all import * ImportError: No module named graph_tool.all I guess I have to tell python where to find the module, but I don't know how to do it Help, please!

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Configure error python development version needed??
by jsia18 20 Feb '12

20 Feb '12

I'm running centos 6.0 Using python 2.7 and boost 1.44 installed numpy scipy, expat and other dependencies when I run configure ./configure --prefix=/opt LDFLAGS=-L/opt/lib CPPFLAGS=-I/opt/include CXXFLAGS=-I/opt/include I am producing an error: (I have Python.h installed since I compiled python2.7 from source) checking consistency of all components of python development environment... no configure: error: Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable. Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib" ============================================================================ ERROR! You probably have to install the development version of the Python package for your distribution. The exact name of this package varies among them. ============================================================================ -- 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.

1 0

Ubuntu first configuration - Price Network example
by Fabio 13 Feb '12

13 Feb '12

Hello, I'm really really new to Ubuntu and Python, so be gentle with me, and moreover don't give anything for granted with me, thank you! I installed graph tool via 'sudo apt-get install graph-tool', and everything seemed to go fine. I'm now trying to run the example code from the documentation (Price Network example), but I cannot make it work :-( These are the steps I followed: 1 - sudo gedit first.py 2 - copy and paste of example code 3 - save (so it gets in my home) 4 - python first.py Here I get the following error: /Traceback (most recent call last): File "first.py", line 10, in <module> from graph_tool.all import * ImportError: No module named graph_tool.all/ I tried the following: 1: reissue the installing command, but it says that graph-tool is already installed with last version 2: if I write 'graph-tool --help' it says command not found 3: gcc -v says /Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3) / 4: python -v says /# installing zipimport hook import zipimport # builtin # installed zipimport hook # /usr/lib/python2.7/site.pyc matches /usr/lib/python2.7/site.py import site # precompiled from /usr/lib/python2.7/site.pyc # /usr/lib/python2.7/os.pyc matches /usr/lib/python2.7/os.py import os # precompiled from /usr/lib/python2.7/os.pyc import errno # builtin import posix # builtin # /usr/lib/python2.7/posixpath.pyc matches /usr/lib/python2.7/posixpath.py import posixpath # precompiled from /usr/lib/python2.7/posixpath.pyc # /usr/lib/python2.7/stat.pyc matches /usr/lib/python2.7/stat.py import stat # precompiled from /usr/lib/python2.7/stat.pyc # /usr/lib/python2.7/genericpath.pyc matches /usr/lib/python2.7/genericpath.py import genericpath # precompiled from /usr/lib/python2.7/genericpath.pyc # /usr/lib/python2.7/warnings.pyc matches /usr/lib/python2.7/warnings.py import warnings # precompiled from /usr/lib/python2.7/warnings.pyc # /usr/lib/python2.7/linecache.pyc matches /usr/lib/python2.7/linecache.py import linecache # precompiled from /usr/lib/python2.7/linecache.pyc # /usr/lib/python2.7/types.pyc matches /usr/lib/python2.7/types.py import types # precompiled from /usr/lib/python2.7/types.pyc # /usr/lib/python2.7/UserDict.pyc matches /usr/lib/python2.7/UserDict.py import UserDict # precompiled from /usr/lib/python2.7/UserDict.pyc # /usr/lib/python2.7/_abcoll.pyc matches /usr/lib/python2.7/_abcoll.py import _abcoll # precompiled from /usr/lib/python2.7/_abcoll.pyc # /usr/lib/python2.7/abc.pyc matches /usr/lib/python2.7/abc.py import abc # precompiled from /usr/lib/python2.7/abc.pyc # /usr/lib/python2.7/_weakrefset.pyc matches /usr/lib/python2.7/_weakrefset.py import _weakrefset # precompiled from /usr/lib/python2.7/_weakrefset.pyc import _weakref # builtin # /usr/lib/python2.7/copy_reg.pyc matches /usr/lib/python2.7/copy_reg.py import copy_reg # precompiled from /usr/lib/python2.7/copy_reg.pyc # /usr/lib/python2.7/traceback.pyc matches /usr/lib/python2.7/traceback.py import traceback # precompiled from /usr/lib/python2.7/traceback.pyc # /usr/lib/python2.7/sysconfig.pyc matches /usr/lib/python2.7/sysconfig.py import sysconfig # precompiled from /usr/lib/python2.7/sysconfig.pyc # /usr/lib/python2.7/re.pyc matches /usr/lib/python2.7/re.py import re # precompiled from /usr/lib/python2.7/re.pyc # /usr/lib/python2.7/sre_compile.pyc matches /usr/lib/python2.7/sre_compile.py import sre_compile # precompiled from /usr/lib/python2.7/sre_compile.pyc import _sre # builtin # /usr/lib/python2.7/sre_parse.pyc matches /usr/lib/python2.7/sre_parse.py import sre_parse # precompiled from /usr/lib/python2.7/sre_parse.pyc # /usr/lib/python2.7/sre_constants.pyc matches /usr/lib/python2.7/sre_constants.py import sre_constants # precompiled from /usr/lib/python2.7/sre_constants.pyc # /usr/lib/python2.7/sitecustomize.pyc matches /usr/lib/python2.7/sitecustomize.py import sitecustomize # precompiled from /usr/lib/python2.7/sitecustomize.pyc # /usr/lib/python2.7/dist-packages/apport_python_hook.pyc matches /usr/lib/python2.7/dist-packages/apport_python_hook.py import apport_python_hook # precompiled from /usr/lib/python2.7/dist-packages/apport_python_hook.pyc import encodings # directory /usr/lib/python2.7/encodings # /usr/lib/python2.7/encodings/__init__.pyc matches /usr/lib/python2.7/encodings/__init__.py import encodings # precompiled from /usr/lib/python2.7/encodings/__init__.pyc # /usr/lib/python2.7/codecs.pyc matches /usr/lib/python2.7/codecs.py import codecs # precompiled from /usr/lib/python2.7/codecs.pyc import _codecs # builtin # /usr/lib/python2.7/encodings/aliases.pyc matches /usr/lib/python2.7/encodings/aliases.py import encodings.aliases # precompiled from /usr/lib/python2.7/encodings/aliases.pyc # /usr/lib/python2.7/encodings/utf_8.pyc matches /usr/lib/python2.7/encodings/utf_8.py import encodings.utf_8 # precompiled from /usr/lib/python2.7/encodings/utf_8.pyc Python 2.7.2+ (default, Oct 4 2011, 20:03:08) [GCC 4.6.1] on linux2 Type "help", "copyright", "credits" or "license" for more information. dlopen("/usr/lib/python2.7/lib-dynload/readline.so", 2); import readline # dynamically loaded from /usr/lib/python2.7/lib-dynload/readline.so/ 5: if I look for graph-tool on the computer, there are two folders in usr/share/doc and usr/doc 6: If I look for python on the computer, I see there is both python2.6 and python2.7 and python3 under usr/lib 7: May it depend on the first row of the code? (#! /usr/bin/env python) Should it refer to some place in particular? Feel free to ask for any extra configuration, but if I need to write some commands, please state them clearly, since I'm a newbie! Thank you very much! Fabio -- 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 2012