graph-tool December 2016

graph-tool@skewed.de

14 participants
24 discussions

Counting the number of leaves at different times
by gogurt 07 Dec '16

07 Dec '16

Hi all, I have a temporal graph G carrying a vertex property map 'time' which is an integer representing the order in which vertices joined the graph. For each integer time from 1 until n (n = the final size of the graph) I want to calculate the number of leaves which exist in the graph up until that time. The problem is that at different point of times in the graph, vertices which were previously leaves can be attached to and thus stop being leaves. So my thought is: For each time t (running from 1 until n): 1) create a GraphView g of the existing graph up until time t 2) count the number of leaves in g To do 1) I would just use the property map 'time'<t. For 2), I would just sum a list comprehension on the map returned by g.degree_property_map(). Is there a more efficient way to do this in graph-tool? I'm still relatively new to the intricacies of graph-tool, and I can see this taking a while with large graphs of a couple million nodes. -- 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 7

RedHat Installation Assistance
by bloodymeli 06 Dec '16

06 Dec '16

Dear All, I have requested out IT manager to install graph-tool on our local cluster (based on RedHat). He changed the "configure" link to point to the corresponding directories, and the "configure" operation seemed to completed successfully. However, the make operation failed with the corresponding message: In file included from ./../graph_python_interface.hh:48:0, from graph_motifs.cc:26: ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_vector_owned(const std::vector<_RealType>&)’: ./../numpy_bind.hh:83:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:83:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:84:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in this scope NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:84:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:84:64: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:84:64: 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<_RealType>&)’: ./../numpy_bind.hh:101:33: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray,NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:101:53: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray,NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:102:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:102:44: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_multi_array_owned(const boost::multi_array<ValueType, Dim>&)’: ./../numpy_bind.hh:122:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:122:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:123:25: error: ‘NPY_ARRAY_OWNDATA’ was not declared in this scope NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:123:45: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:123:64: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] NPY_ARRAY_OWNDATA | NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh: In function ‘boost::python::api::object wrap_multi_array_not_owned(boost::multi_array<ValueType, Dim>&)’: ./../numpy_bind.hh:137:34: error: ‘NPY_ARRAY_ALIGNED’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:137:54: error: ‘NPY_ARRAY_C_CONTIGUOUS’ was not declared in this scope PyArray_ENABLEFLAGS(ndarray, NPY_ARRAY_ALIGNED | NPY_ARRAY_C_CONTIGUOUS | ^ ./../numpy_bind.hh:138:25: error: ‘NPY_ARRAY_WRITEABLE’ was not declared in this scope NPY_ARRAY_WRITEABLE); ^ ./../numpy_bind.hh:138:44: error: there are no arguments to ‘PyArray_ENABLEFLAGS’ that depend on a template parameter, so a declaration of ‘PyArray_ENABLEFLAGS’ must be available [-fpermissive] NPY_ARRAY_WRITEABLE); ^ make[4]: *** [graph_motifs.lo] Error 1 make[4]: Leaving directory `/usr/local/graph-tool-2.19/src/graph/clustering' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/usr/local/graph-tool-2.19/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/graph-tool-2.19/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/graph-tool-2.19' make: *** [all] Error 2 Any idea how to resolve this? -- 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 11

Way to get vertex ids that belong to a group
by COMEGETME 06 Dec '16

06 Dec '16

After running an inference method such as: graph_tool.inference.minimize_blockmodel_dl() I get back a graph_tool.inference.BlockState, which provides a PropertyMap on the vertices which i can use to tell which group a vertex is in. However, if i need to find out all the other members of the same group, (suppose i need to find out who/what else is in the same group as a particular vertex, is there a way to list the groups members other than looping though all vertices and querying their group in the Propertymap? As a bonus, i have a bit of a background in scientific application support as a scientist+sysadmin, so here are Fedora 23/24 graph_tool packages for the Fedora users out there, made with love using the opensuse OBS. http://download.opensuse.org/repositories/home:/theusprom1/Fedora_23/ http://download.opensuse.org/repositories/home:/theusprom1/Fedora_24/ For more info look here: https://build.opensuse.org/package/show/home:theusprom1/graph-tool I second your advise to use the prebuilt packages that the project has already provided, the compile time resources needed are non trivial :(https://build.opensuse.org/package/statistics/home:theusprom1/graph-tool?arch=x86_64&repository=Fedora_24). I have used these packages (im just getting started though), so YMMV. Best. Theos.

2 1

Issue will gt.topology.all_paths()
by Evangelos Petsalis 01 Dec '16

01 Dec '16

Hi, I am running graph-too v2.18 on Ubuntu 15.10 and I was trying to to use the all_paths() function but when I run the example code (or any other code for that matter) I keep getting the following error: Traceback (most recent call last): File "/usr/lib/python3.4/code.py", line 90, in runcode exec(code, self.locals) File "<input>", line 1, in <module> File "/usr/lib/python3/dist-packages/graph_tool/topology/__init__.py", line 1732, in all_paths _prop("v", g, visited)) RuntimeError: This functionality is not available because boost::coroutine was not found at compile-time Did I compile the graph-tool the wrong way or is it a problem with the function itself? Regards, Vaggelis

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graph-tool December 2016