graph-tool February 2017

graph-tool@skewed.de

13 participants
30 discussions

Random graph generation in graph-tool
by Snehal Shekatkar 13 Feb '17

13 Feb '17

Dear all, This must be a quite studip question. I am slightly confused about the random graph generation in graph-tool. So I tried generating an ER network: def deg_samp(k0 = 3): return np.random.poisson(k0) G = gt.random_graph(500, lambda : deg_samp(3), directed = False) This gives reasonable result: <Graph object, undirected, with 500 vertices and 780 edges at 0x7f516e897f98> However, I think that the following call is equivalent: G = gt.random_graph(500, deg_samp, directed = False) But this results into an extremely dense graph: <Graph object, undirected, with 500 vertices and 62252 edges at 0x7f516e8b59b0> What am I missing exactly? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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Getting all unique values in a vector-valued vertex property map
by gogurt 12 Feb '17

12 Feb '17

This might be a stupid question, but I have a graph with a vector<str>-valued vertex property map. That is, each vertex has a vector containing one or more strings encoding some metadata about the vertex. I want to get a single 1d-list/array containing all the unique string values encoded in this property map, over all vertices in the graph. What's the best way to do that? I know that I'll have to use the get_2d_array() method on the property map, but I can't really understand what the documentation means when it says: "The parameter pos must be a sequence of integers which specifies the *indexes of the property values which will be used.*" -- 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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Correlation Histogram
by P-M 12 Feb '17

12 Feb '17

I am trying to obtain the correlation histogram for a graph of mine following the example given in the manual. I run: g = gt.load_graph('graph.gt') gt.remove_parallel_edges(g) h=gt.corr_hist(g,'out','out') My graph is relatively large at 12,238,931 vertices and 24,884,365 edges. My problem is that as soon as I start the code it runs on 20 processes and happily chomps through 252 GB of RAM before starting to spill over into the swap making my machine incredibly slow. I presume the RAM usage is linked to the parallel processing so presumably could be tackled if I ran it using fewer processes. Is there any way of reducing the RAM usage? Or would I need to implement the routine manually to achieve this? 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.

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Gtk-ERROR while plotting a matrix
by Snehal Shekatkar 11 Feb '17

11 Feb '17

Hello all, I am trying to plot the matrix representation of inferred blocks. state = gt.minimize_blockmodel_dl(G, deg_corr=True) e = state.get_matrix() plt.matshow(e.todense()) However, this throws an error: (ipython:14458): Gtk-ERROR **: GTK+ 2.x symbols detected. Using GTK+ 2.x and GTK+ 3 in the same process is not supported Trace/breakpoint trap (core dumped) I am not sure what is happening. Any help? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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Colorbar in graph-tool
by Snehal Shekatkar 08 Feb '17

08 Feb '17

Dear Tiago, I am trying to draw a graph in which edges have some property of type float. I am coloring the edges using these float values. Now, I want to show a colorbar on the side of the graph which would give idea of these values on the edges. Is this possible in any way? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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Could not link against boost_coroutine
by dperry324 07 Feb '17

07 Feb '17

Hello, I'm having an issue with trying to compile graph-tool 2.20 on RedHat 6.6 using python 2.7.8. I downloaded, compiled and installed boost 1.61 into /usr/local/boost161 The configure routine seems to be finding the Boost::Coroutine library just fine. The problem is when it tests the library it finds and it fails. I run the command like so: # ./configure --with-boost=/usr/local/boost161 =========================== Using python version: 2.7.8 =========================== checking for boostlib >= 1.54.0... 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::Coroutine library is available... yes checking for exit in -lboost_coroutine... no checking for exit in -lboost_coroutine... (cached) no configure: error: Could not link against boost_coroutine ! This to me seems like it is a problem with boost installation, and not graph-tool. But I can find no references to this being an issue, so I'm wondering if this is something that is known. If it's known, I'm hoping there's a fix for it. Is there any thought as to why this fails? -- 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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Hacking sfdp to properly show large graphs
by gogurt 07 Feb '17

07 Feb '17

Hi all, I'm trying to visualize some large (>100k vertices) graphs using graph-tool, but I'm having trouble getting a good picture with the sfdp layout. I'm unsure about is whether this is due to me not knowing how to use sfdp_layout(), or whether it's just impossible lay out large graphs efficiently due to the topology. Here's a sample graph of what I'm talking about. I'm uploaded it in xml format here: https://www.dropbox.com/s/5zg4u9re9rw6s4y/test.xml.gz?dl=0 It's about 100k vertices and max degree ~ 2400 and average degree ~ 7.8. Obviously, this will be hard to graph. Anyway, when I draw the graph using the standard method: pos = gt.sfdp_layout(G) gt.graph_draw(G, pos=pos) Then I get a graph that looks like this: <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> The vertices are tiny. Which makes sense, because otherwise with the If I increase the vertex size by supplying vprops={'size': 2} (for example) to gt.graph_draw(), then I just get a huge blob. My question: is it possible to force sfdp to space out the vertices more so that I can increase the vertex size *and* have them not all coalesce into one giant blob? -- 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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general "did not match C++ signature" error
by bloodymeli 07 Feb '17

07 Feb '17

Hi, Graph-tool was manually compiled on a local cluster (based on RedHat) by a network admin. The python command import graph_tool works fine, but almost every other command results in an error related to "did not match C++ signature": For example, gtGraph=graph_tool.load_graph("yeast.graphml") (attached) results in: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py", line 2702, in load_graph g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp) File "/usr/local/epd/lib/python2.7/site-packages/graph_tool/__init__.py", line 2320, in load ignore_ep, ignore_gp) Boost.Python.ArgumentError: Python argument types in GraphInterface.read_from_file(GraphInterface, str, NoneType, str, list, list, list) did not match C++ signature: read_from_file(graph_tool::GraphInterface {lvalue}, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, boost::python::api::object, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, boost::python::list, boost::python::list, boost::python::list) Following some other posts in the mailing list, I've applied the ldd command and: ldd /usr/local/epd/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so linux-vdso.so.1 => (0x00007ffff7ffe000) libboost_iostreams.so.1.59.0 => /usr/lib64/libboost_iostreams.so.1.59.0 (0x00007ffff5c46000) libboost_python.so.5 => /usr/lib64/libboost_python.so.5 (0x00007ffff59f5000) libboost_regex.so.1.59.0 => /usr/lib64/libboost_regex.so.1.59.0 (0x00007ffff56df000) libboost_coroutine.so.1.59.0 => /usr/lib64/libboost_coroutine.so.1.59.0 (0x00007ffff54d4000) libCGAL.so.12 => /usr/local/cgal-releases-CGAL-4.9/build/release/lib/libCGAL.so.12 (0x00007ffff52af000) libexpat.so.1 => /lib64/libexpat.so.1 (0x00007ffff5087000) libstdc++.so.6 => /usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libstdc++.so.6 (0x00007ffff4cf8000) libm.so.6 => /lib64/libm.so.6 (0x00007ffff4a74000) libc.so.6 => /lib64/libc.so.6 (0x00007ffff46e0000) libgcc_s.so.1 => /usr/local/gcc5.3/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/libgcc_s.so.1 (0x00007ffff44c9000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ffff42b8000) libz.so.1 => /usr/local/epd/lib/libz.so.1 (0x00007ffff409a000) librt.so.1 => /lib64/librt.so.1 (0x00007ffff3e91000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ffff3c74000) libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007ffff38ce000) libicudata.so.42 => /usr/lib64/libicudata.so.42 (0x00007ffff2788000) libicui18n.so.42 => /usr/lib64/libicui18n.so.42 (0x00007ffff23f2000) libicuuc.so.42 => /usr/lib64/libicuuc.so.42 (0x00007ffff20a0000) libboost_context.so.1.59.0 => /usr/lib64/libboost_context.so.1.59.0 (0x00007ffff1e96000) libboost_thread.so.1.59.0 => /usr/lib64/libboost_thread.so.1.59.0 (0x00007ffff1c74000) libboost_chrono.so.1.59.0 => /usr/lib64/libboost_chrono.so.1.59.0 (0x00007ffff1a6d000) libboost_system.so.1.59.0 => /usr/lib64/libboost_system.so.1.59.0 (0x00007ffff1869000) libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x00007ffff161c000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007ffff13c1000) /lib64/ld-linux-x86-64.so.2 (0x0000003f14800000) libdl.so.2 => /lib64/libdl.so.2 (0x00007ffff11bc000) libutil.so.1 => /lib64/libutil.so.1 (0x00007ffff0fb9000) yeast.graphml <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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graph_draw clipping issues
by Steve 05 Feb '17

05 Feb '17

How do I fix clipping issues with graph_draw when they arise? Here's a minimal example that shows some clipping of the self-loops. I have this issue occasionally with mor complicated graphs too. edge_list = [ (0,1), (1,2), (2,0), (0,2), (1,1), (2,2) ] g = gt.Graph() g.add_edge_list(edge_list) pos = gt.sfdp_layout(g) gt.graph_draw(g,pos=pos,vertex_text=g.vertex_index) I've tried fit_view options and rescaling pos by hand, all to no avail. -- 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 1

Use images as vertex symbols in graph_draw
by P-M 02 Feb '17

02 Feb '17

This is a somewhat general question but perhaps somebody can point me in a useful direction: I am trying to draw a small network of molecules. Ideally I would like to use the molecular structures (which I can save as image file) in the network representation as opposed to the normal little red circles. Is it possible to specify a separate file for each vertex that gets used as position marker? I have found "surface" as a vertex property in "graph_draw" but am not sure if that is what I am after. 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.

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graph-tool February 2017