graph-tool October 2013

graph-tool@skewed.de

8 participants
19 discussions

how to access Source Network file: pgp.xml.gz?
by Carlos Carroll 25 Oct '13

25 Oct '13

Is there an alternate link for the Source Network file ( pgp.xml.gz<http://graph-tool.skewed.de/static/performance/pgp.xml.gz> ) for the performance test at http://graph-tool.skewed.de/performance When I try the current link, it just gives me a webpage with content as below, but no working links: Performance: pgp.xml.gz File pgp.xml.gz, 2.0 MB (added by tiago peixoto, 6 months ago) Strongly connected component of the PGP network circa 2009. HTML preview not available, since the file size exceeds 262144 bytes. Try downloading the file instead. Download in other formats: Original Format

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Closeness not included in module
by poydflink 22 Oct '13

22 Oct '13

Hi there, when I try to calculate the closeness metric it says it's not in the module. I have tried to import it and in fact I cannot find it, simply put. I can correctly calculate all the other centralities. Was it added very recently maybe, and I don't have the latest version? Thanks in advance -- 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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Pearson Correlation Coefficient
by poydflink 22 Oct '13

22 Oct '13

Hi there, I'd like to know if this is the method used to calculate the average neighbhoor correlation (http://graph-tool.skewed.de/static/doc/correlations.html#graph_tool.correla… ). Or any correlation used by the module, in fact. Thank you in advance! -- 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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TypeError from purge_vertices()
by Mark Howell 21 Oct '13

21 Oct '13

I am trying to use purge_vertices() with a vertex filter to efficiently remove vertices from a graph. I am seeing different behavior in version 2.2.18 and 2.2.25, both as prebuilt packages for Ubuntu precise (current "graph-tool" and "python-graph-tool" packages, respectively) I have a simple example script attached which shows the behavior. If I run with graph-tool 2.2.18, it works without complaint, e.g.: $ python graph-tool-play2.py graph_tool version 2.2.18 (commit 83bb8a49, Tue Nov 13 00:57:29 2012 +0100) pruning 11 pruning 13 pruning 14 pruning 19 pruning 23 pruning 26 pruning 46 pruning 47 pruning 48 pruning 52 pruning 63 pruning 81 pruning 93 pruning 97 complete If I run with python-graph-tool 2.2.25, I get a TypeError, e.g.: $ python graph-tool-play2.py graph_tool version 2.2.25 (commit feec13d9, Mon Sep 2 00:01:39 2013 +0200) pruning 10 pruning 12 pruning 13 pruning 18 pruning 22 pruning 25 pruning 45 pruning 46 pruning 47 pruning 51 pruning 62 pruning 80 pruning 92 pruning 96 Traceback (most recent call last): File "graph-tool-play2.py", line 59, in <module> g.purge_vertices() # MJH this will die in graph-tool 2.2.25 with a TypeError. Works in 2.2.18. File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1838, in purge_vertices new_g = Graph(self, prune=(True, False, False)) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1109, in __init__ vorder.fa = numpy.arange(gv.num_vertices()) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 561, in <lambda> lambda self, v: self.__get_set_f_array(v, False), File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 556, in __get_set_f_array a[m] = v TypeError: array cannot be safely cast to required type Why would this fail in 2.2.25? It's entirely possible that I am missing something basic about how to fly graph-tool. Any clues appreciated! Cheers, Mark.

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Mac OS X 10.8 $make error
by Nikita Fedkin 15 Oct '13

15 Oct '13

Hello, i'am trying to install graph-tool to my mac(building from source) and getting this while compilation: Any ideas what i can do with that? make all-recursive Making all in src Making all in graph Making all in centrality CXX graph_betweenness.lo warning: unknown warning option '-Wno-unused-local-typedefs' [-Wunknown-warning-option] In file included from graph_betweenness.cc:18: In file included from ./../graph_filtering.hh:52: ./../graph_adaptor.hh:142:41: error: no template named 'is_convertible' in namespace 'std::tr1'; did you mean 'is_convertible'? typedef typename mpl::if_<std::tr1::is_convertible<typename std::ite... ~~~~~~~~~~^~~~~~~~~~~~~~ is_convertible /usr/local/include/boost/type_traits/is_convertible.hpp:484:30: note: 'is_convertible' declared here BOOST_TT_AUX_BOOL_TRAIT_DEF2(is_convertible,From,To,BOOST_IS_CONVERTIBLE... ^ /usr/local/include/boost/type_traits/detail/bool_trait_def.hpp:81:45: note: expanded from macro 'BOOST_TT_AUX_BOOL_TRAIT_DEF2' template< typename T1, typename T2 > struct trait \ ^ 1 warning and 1 error generated. make[4]: *** [graph_betweenness.lo] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2

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edge property for weighted search with vertex property for max_dist cutoff.
by Tasos Varoudis 14 Oct '13

14 Oct '13

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make (--enable-openmp) problem error1, error2
by lolkasasa＠gmail.com 14 Oct '13

14 Oct '13

Hello, i am trying to compile graph-tool for parallel mode and getting this error, while doing $make. Can you help me? make all-recursive make[1]: Entering directory `/home/smith/local/graph-tool-2.2.25' Making all in src make[2]: Entering directory `/home/smith/local/graph-tool-2.2.25/src' Making all in graph make[3]: Entering directory `/home/smith/local/graph-tool-2.2.25/src/graph' Making all in centrality make[4]: Entering directory `/home/smith/local/graph-tool-2.2.25/src/graph/centrality' CXX graph_closeness.lo In file included from graph_closeness.hh:29:0, from graph_closeness.cc:23: ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_vector_owned(std::vector<ValueType>&)’: ./../numpy_bind.hh:78:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope ./../numpy_bind.hh:78:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope ./../numpy_bind.hh:79:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in this scope ./../numpy_bind.hh:79:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope ./../numpy_bind.hh:79:64: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] ./../numpy_bind.hh:79:64: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated) ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_vector_not_owned(std::vector<ValueType>&)’: ./../numpy_bind.hh:96:33: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope ./../numpy_bind.hh:96:53: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope ./../numpy_bind.hh:97:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope ./../numpy_bind.hh:97:44: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_multi_array_owned(boost::multi_array<ValueType, Dim>&)’: ./../numpy_bind.hh:116:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope ./../numpy_bind.hh:116:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope ./../numpy_bind.hh:117:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in this scope ./../numpy_bind.hh:117:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope ./../numpy_bind.hh:117:64: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_multi_array_not_owned(boost::multi_array<ValueType, Dim>&)’: ./../numpy_bind.hh:130:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope ./../numpy_bind.hh:130:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope ./../numpy_bind.hh:131:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope ./../numpy_bind.hh:131:44: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] ./../numpy_bind.hh: In function ‘boost::multi_array_ref<ValueType, dim> get_array(boost::python::api::object)’: ./../numpy_bind.hh:173:30: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope At global scope: cc1plus: warning: unrecognized command line option "-Wno-unused-local-typedefs" [enabled by default] make[4]: *** [graph_closeness.lo] Error 1 make[4]: Leaving directory `/home/smith/local/graph-tool-2.2.25/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/smith/local/graph-tool-2.2.25/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/smith/local/graph-tool-2.2.25/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/smith/local/graph-tool-2.2.25' make: *** [all] Error 2

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loading in graphs, property map issue
by John Hirdt 14 Oct '13

14 Oct '13

I have created a graph in xml format and saved this graph. When I go to load in graph, I am successful but the property maps are no longer populated as they were when I created the graph. All bool values go to 0, all ints go to 0 and all strings go to '' Any idea why this is happening and how I can successfully load in both the graph and the populated property maps? Thanks John Hirdt

2 1

edge property for weighted search with vertex property for max_dist cutoff
by Tasos 11 Oct '13

11 Oct '13

Hi all, How can I use a vertex property for search cutoff on graphs that are weighted based on an edge property? I want the search to visit the vertex based on the edge weights but the cutoff to be based on a vertex property. Thanks Tasos -- 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 October 2013