June 2016 - graph-tool - archives.skewed.de

Installation error: graph_triangulation.Io
by Yu Zheng 28 Jun '16

28 Jun '16

Having installed every pre-requisite, including CGAL on my Linux server, I still encounter the following error during installation. The specific error message is: */usr/local/include/CGAL/Periodic_3_Delaunay_triangulation_3.h:266:60:* *error: *no match for call to ‘*(CGAL::internal::Static_filters<CGAL::Filtered_kernel_base<CGAL::Type_equality_wrapper<CGAL::Cartesian_base_no_ref_count<double, CGAL::Epick>, CGAL::Epick> >, false>::Side_of_oriented_sphere_3 {aka CGAL::internal::Static_filters_predicates::Side_of_oriented_sphere_3<CGAL::Filtered_kernel_base<CGAL::Type_equality_wrapper<CGAL::Cartesian_base_no_ref_count<double, CGAL::Epick>, CGAL::Epick> > >}) (const Point&, const Point&, const Point&, const Point&, const Point&, const Offset&, const Offset&, const Offset&, const Offset&, const Offset&)*’ I have included the log file for configuration and make here. Thanks a lot for your help!

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Re: [graph-tool] Anaconda boost and ubuntu
by Rogelio Basurto 23 Jun '16

23 Jun '16

Hi Philipp, Have you tried done the importing without Anaconda? Open a terminal, write python (and/or python3, depends on the python version you use), enter and write the importing "from graph_tool.all import *". Does give you the same error? I am no expert, but I hope this gives you some light. ____ *Rogelio Basurto Flores* Laboratorio de Sistemas Complejos *Unidad Profesional Interdisciplinaria en Ingeniería y * *Tecnologías Avanzadas,* *Instituto Politécnico Nacional,* *Av. IPN # 2580, Col. Laguna Ticoman,* *Mexico D. F., 07340, Mexico* *Mobile Phone: 33 1551 3665* *E-Mail: rogelio.basurto(a)gmail.com <rogelio.basurto(a)gmail.com>* On Thu, Jun 23, 2016 at 5:00 AM, <graph-tool-request(a)skewed.de> wrote: > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. libboost_iostreams.so.1.61.0: cannot open shared object file: > No such file or directory (P-M) > 2. Re: libboost_iostreams.so.1.61.0: cannot open shared object > file: No such file or directory (ostrokach) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Jun 2016 08:36:30 -0700 (MST) > From: P-M <pmj27(a)cam.ac.uk> > To: graph-tool(a)skewed.de > Subject: [graph-tool] libboost_iostreams.so.1.61.0: cannot open shared > object file: No such file or directory > Message-ID: <1466609790258-4026599.post(a)n3.nabble.com> > Content-Type: text/plain; charset=us-ascii > > I am using Anaconda as my main python distribution (though also have the > system's default python installed) so have to compile graph-tool from > source > to get it to work with Anaconda. I am using Ubuntu 14.04 so also have to > compile boost from source to be able to use the full functionality of > graph-tool. I have done so and they have both installed without any error > messages, however, when then importing graph-tool in python using `from > graph_tool.all import *` I get the error message `ImportError: > libboost_iostreams.so.1.61.0: cannot open shared object file: No such file > or directory`. > > How could I go about solving that problem/what is this caused by? > > Best wishes, > > Philipp > > > > -- > 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. > > > ------------------------------ > > Message: 2 > Date: Wed, 22 Jun 2016 15:41:35 -0700 (MST) > From: ostrokach <ostrokach(a)gmail.com> > To: graph-tool(a)skewed.de > Subject: Re: [graph-tool] libboost_iostreams.so.1.61.0: cannot open > shared object file: No such file or directory > Message-ID: > < > CAK3HUpg7NPxY__sQ2UEdgcDL7jsa9868_LH0J97tyTKfircRVg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Do you have libboost_iostreams.so.1.61.0 in your anaconda/lib folder? > ? > > On Wed, Jun 22, 2016 at 11:36 AM, P-M [via Main discussion list for the > graph-tool project] <ml-node+s982480n4026599h93(a)n3.nabble.com> wrote: > > > I am using Anaconda as my main python distribution (though also have the > > system's default python installed) so have to compile graph-tool from > > source to get it to work with Anaconda. I am using Ubuntu 14.04 so also > > have to compile boost from source to be able to use the full > functionality > > of graph-tool. I have done so and they have both installed without any > > error messages, however, when then importing graph-tool in python using > > `from graph_tool.all import *` I get the error message `ImportError: > > libboost_iostreams.so.1.61.0: cannot open shared object file: No such > file > > or directory`. > > > > How could I go about solving that problem/what is this caused by? > > > > Best wishes, > > > > Philipp > > > > ------------------------------ > > If you reply to this email, your message will be added to the discussion > > below: > > > > > http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… > > To unsubscribe from Main discussion list for the graph-tool project, > click > > here > > < > http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… > > > > . > > NAML > > < > http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… > > > > > > > > > -- > 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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About Debian installation
by ibirisol＠dcc.ufba.br 16 Jun '16

16 Jun '16

Hi there, The section Debian installation on graph-tool download page [1] is not working. The reason of that is a mirror url [2] redirect from http to https. To solve this problem I suggest: You explain accurately every necessary steps to install graph-tool, including (before mirror update) a instruction to install apt-transport-https package or, another possible way to solve this, you simply remove the 'redirect' from the mirror page. [1] https://graph-tool.skewed.de/download [2] http://downloads.skewed.de/apt Best regards,

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Help with "Make" for linux - CentOS 7
by yz2235 16 Jun '16

16 Jun '16

config.rtf <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Log_make.rtf <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Dear all, I am an Economics Ph.D student, trying to install graph-tool-2.16 on a linux - CentOS7 server. I have carefully checked all the prerequisite for installation, and searched the mailing archive, but cannot seem to find a solution to my particular error message when I issue the command "make". I have attached "config.log" file as well as the error message that popped up after the command "make" for your review. Thank you very much for your help. And I apologize in advance if this turned out to be some duplicate. Being a non-CS person, the best I could do to check duplicates is by searching the exact same error message. Much obliged, Yu -- 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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Surprising run time increase
by François 08 Jun '16

08 Jun '16

Hello, For experimental purpose I benchmarked the *topology.shortest_distance* run time. I stumbled upon something I fail to explain. In this benchmark I compare two graphs : (*) The first graph is undirected and has about 11M edges and 8M vertices; (*) The second graph is a copy of the first one with directed edges. In this graph, for each edge from the first graph the backward edge is added. Hence, the second graph has about 22M edge and 8M vertices. I use https://gist.github.com/Fkawala/f7a3366a0d702163d7499ce29efec78e <https://gist.github.com/Fkawala/f7a3366a0d702163d7499ce29efec78e> to measure the run time of a shortest path to all vertices within a given distance. With the first graph the run time is : ncalls tottime percall cumtime percall filename:lineno(function) 1 0.035 0.035 0.060 0.060 graph_tool/topology/__init__.py:1272(shortest_distance) 1 0.000 0.000 0.019 0.019 graph_tool/decorators.pyc:1(copy_property) 2/1 0.000 0.000 0.019 0.019 graph_tool/decorators.py:126(wrapper) 1 0.013 0.013 0.019 0.019 graph_tool/__init__.py:2247(copy_property) 10 0.000 0.000 0.011 0.001 graph_tool/__init__.py:146(_prop) 8 0.000 0.000 0.011 0.001 graph_tool/__init__.py:476(_get_any) 8 0.011 0.001 0.011 0.001 graph_tool/__init__.py:893(reserve) 1 0.000 0.000 0.001 0.001 graph_tool/__init__.py:2559(set_edge_filter) 1 0.000 0.000 0.001 0.001 graph_tool/__init__.py:680(__set_array) 1 0.000 0.000 0.000 0.000 graph_tool/__init__.py:643(get_array) 4 0.000 0.000 0.000 0.000 graph_tool/__init__.py:667(_get_data) [truncated] With the second graph the run is : ncalls tottime percall cumtime percall filename:lineno(function) 1 2.347 2.347 2.372 2.372 graph_tool/topology/__init__.py:1272(shortest_distance) 1 0.000 0.000 0.019 0.019 graph_tool/decorators.pyc:1(copy_property) 2/1 0.000 0.000 0.019 0.019 graph_tool/decorators.py:126(wrapper) 1 0.012 0.012 0.018 0.018 graph_tool/__init__.py:2247(copy_property) 9 0.000 0.000 0.011 0.001 graph_tool/__init__.py:146(_prop) 5 0.000 0.000 0.011 0.002 graph_tool/__init__.py:476(_get_any) 5 0.011 0.002 0.011 0.002 graph_tool/__init__.py:893(reserve) 1 0.001 0.001 0.001 0.001 graph_tool/__init__.py:975(_check_prop_scalar) [truncated] How could we explain this difference? I there a something to do to reduce the run time observed with the second graph ? Bests, F. -- 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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Questions about inference algorithms
by Andrea Briega 08 Jun '16

08 Jun '16

Dear Dr Peixoto, I would like to solve some questions I have about inference algorithms for the identification of large-scale network structure via the statistical inference of generative models. Minimize_blockmodel algorithm takes an hour to finish using my network with 21000 nodes (like the hierarchical version), and it spends two days and a half with overlap. However, I have run an hierarchical analysis with overlap, and it is still running since 14 days ago. So my first question is: is this time normal, or maybe there is any problem? Do you know how long could it ussually takes? Secondly, I have repeated some of these analysis with exactly same options but I get different solutions (similar but different), so I wonder if the algorithm is heuristic (I thought it was exact). My last question question regards bipartite analysis. I have two types of nodes in my network and I wonder if there are any analytical difference when running these algorithms with the bipartite option (clabel=True, and different labels in each group of nodes) or not, because it seems that the program “knows” my network is bipartite in any case. If there are differences between bipartite and “unipartite” analysis (clabel=False), is it possible to compare description length between them to model selection? Thank you very much for your help! Best regards, Andrea

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Re: [graph-tool] graph-tool Digest, Vol 100, Issue 10
by Rogelio Basurto 02 Jun '16

02 Jun '16

Thanks for the answer Tiago! Have a great week! ____ *Rogelio Basurto Flores* Laboratorio de Sistemas Complejos *Unidad Profesional Interdisciplinaria en Ingeniería y * *Tecnologías Avanzadas,* *Instituto Politécnico Nacional,* *Av. IPN # 2580, Col. Laguna Ticoman,* *Mexico D. F., 07340, Mexico* *Mobile Phone: 33 1551 3665* *E-Mail: rogelio.basurto(a)gmail.com <rogelio.basurto(a)gmail.com>* On Sun, May 29, 2016 at 5:00 AM, <graph-tool-request(a)skewed.de> wrote: > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. Re: About the blocks from the minimize_nested_blockmodel_dl > (Tiago de Paula Peixoto) > 2. Graph-tool configure error: Boost::Iostreams library is > available but no usable boost::iostreams is found (Bretsky) > 3. Re: Graph-tool configure error: Boost::Iostreams library is > available but no usable boost::iostreams is found (Frank Takes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 28 May 2016 13:49:35 +0200 > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: Main discussion list for the graph-tool project > <graph-tool(a)skewed.de> > Subject: Re: [graph-tool] About the blocks from the > minimize_nested_blockmodel_dl > Message-ID: <8d4b53ee-e259-e49b-755a-0f70abace2ea(a)skewed.de> > Content-Type: text/plain; charset="utf-8" > > On 26.05.2016 04:22, Rogelio Basurto wrote: > > I am reading a bipartite network from a graphml file, then I do some > > filtering and finally I construct the minimize_nested_blockmodel_dl as > > in the example. Then I draw it, just like in the example, and it looks > > great. I manage to draw it with the node names and they are fine. > > > > Then, I would like to check the names of the nodes in the different > > blocks, by the levels they are arranged from the stochastic nested > > block model. But I do not know how to do that. > > > > I found the function get_bstack() for the NestedBlockState object, but > > the index in those vertices are from 0 to N, where N is the number of > > vertices per level (of the model, not from my graph, I think), then > > how do I associate my original vertex index (which has its name) to > > those graphs from the different levels? > > The partition of nodes in the first level is obtained via: > > b = state.levels[0].get_blocks() > > This is a vertex property map that says to which block a node of your > network belongs. For example: > > >>> print(b[10]) > 3 > > The above means that vertex 10 belongs to group 3. The same can be done > for the higher levels of the hierarchy, i.e. > > >>> b = state.levels[1].get_blocks() > >>> print(b[3]) > 5 > > The group number 3 in the first level, belongs to group number 5 in the > second level. An so on. > > Best, > Tiago > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > >

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