January 2017 - graph-tool - archives.skewed.de

apt-get fail to download index files
by Andy Maloney 10 Mar '17

10 Mar '17

I am trying to install graph-tool on a Trusty Ubuntu virtualbox being hosted on a Mac. I've added the requisite lines deb http://downloads.skewed.de/apt/trusty trusty main deb-src http://downloads.skewed.de/apt/trusty trusty main to my /etc/apt/sources.list, but when I run a sudo apt-get update, I get the following errors: W: Failed to fetch http://downloads.skewed.de/apt/trusty/dists/trusty/Release Unable to find expected entry 'main/source/Sources' in Release file (Wrong sources.list entry or malformed file) E: Some index files failed to download. They have been ignored, or old ones used instead. I have the main, universe, and multiverse repositories available. If any one has come across this problem before, please let me know how to fix it. Thanks. Andy_

4 4

Some clarifications regarding directness
by bloodymeli 23 Feb '17

23 Feb '17

Hi, Consider the following GraphML file (attached). According to the GraphML file, it represents an undirected graph. Therefore, I would expect that as I set it to directed graph: gtGraph=gt.load_graph("yeast.graphml") gtGraph.set_directed(1) I would obtain two directed edges for every undirected edge. In particular, the in degree of every node should be equal to the out degree. However, this is not the case, for example: v=gtGraph.vertex(1834) v.in_degree() Out[3]: 5 v.out_degree() Out[4]: 2 I'm a bit puzzled. A) Is the source file corrupted? B) When I set the directedness flag to 1, am I guaranteed that every undirected edge would be converted to two directed edges? If not, how can I perform this operation (A = A + A', assuming the adjacency matrix is triangular) or validate it? 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.

3 3

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.

4 8

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.

2 2

self._state.couple_state(state._state, entropy_args) - Python argument types did not match C++ signature
by P-M 30 Jan '17

30 Jan '17

Hello Tiago, I am sorry that I seem to keep on bugging you with error messages. I have been playing around with the inference module a bit and tried to replicate a section of code from your cookbook section. When running gt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10)) I however get an error message. I have attached the code num_groups_marg_prob.py <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> and the screen output screengrab.dat <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> . It seems to revolve around Python argument types not matching C++ signatures. Having done some searching this seems to come up when using different compilers for different modules (?). In this case I am however running the package as downloaded from apt-get (2.19 (commit da041f33, Sat Nov 12 17:27:48 2016 +0100)) so I was surprised to see it. The same error also gets thrown if running it on a compiled version of the source code (2.20dev (commit 01432d60, Sun Jan 15 19:54:52 2017 +0000)). Do you know what is going wrong here/how I could fix it? I have copied the error below as it is quite long. N.B.: This is on a different machine to the one I was posting about earlier (though it has the same issue with cairomm). Traceback (most recent call last): File "num_groups_marg_prob.py", line 26, in <module> gt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10)) File "/usr/lib/python2.7/dist-packages/graph_tool/inference/mcmc.py", line 127, in mcmc_equilibrate delta, nmoves = state.mcmc_sweep(**mcmc_args) File "/usr/lib/python2.7/dist-packages/graph_tool/inference/nested_blockmodel.py", line 576, in mcmc_sweep return self._h_sweep(lambda s, **a: s.mcmc_sweep(**a), c=c, **kwargs) File "/usr/lib/python2.7/dist-packages/graph_tool/inference/nested_blockmodel.py", line 499, in _h_sweep get_entropy_args(eargs)) File "/usr/lib/python2.7/dist-packages/graph_tool/inference/blockmodel.py", line 616, in _couple_state self._state.couple_state(state._state, entropy_args) Boost.Python.ArgumentError: Python argument types in graph_tool::BlockState<boost::adj_list<unsigned long>, graph_tool::simple_degs_t, std::integral_constant<bool, false>, std::integral_constant<bool, false>, boost::any, boost::any, boost::any, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, bool, int, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, double, double, double, double, double, double, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, bool>.couple_state(graph_tool::BlockState<boost::adj_list<unsigned long>, graph_tool::simple_degs_t, std::integral_constant<bool, false>, std::integral_constant<bool, false>, boost::any, boost::any, boost::any, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, bool, int, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, double, double, double, double, double, double, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, bool>, graph_tool::BlockState<boost::adj_list<unsigned long>, graph_tool::simple_degs_t, std::integral_constant<bool, true>, std::integral_constant<bool, false>, boost::any, boost::any, boost::any, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, bool, int, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, double, double, double, double, double, double, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, bool>, entropy_args) did not match C++ signature: couple_state(graph_tool::BlockState<boost::adj_list<unsigned long>, graph_tool::simple_degs_t, std::integral_constant<bool, false>, std::integral_constant<bool, false>, boost::any, boost::any, boost::any, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, bool, int, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, double, double, double, double, double, double, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, bool> {lvalue}, graph_tool::BlockState<boost::adj_list<unsigned long>, graph_tool::simple_degs_t, std::integral_constant<bool, false>, std::integral_constant<bool, false>, boost::any, boost::any, boost::any, boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, std::vector<unsigned long, std::allocator<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<int, boost::typed_identity_property_map<unsigned long> >, bool, int, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::adj_edge_index_property_map<unsigned long> >, boost::unchecked_vector_property_map<double, boost::typed_identity_property_map<unsigned long> >, double, double, double, double, double, double, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, boost::unchecked_vector_property_map<unsigned char, boost::typed_identity_property_map<unsigned long> >, bool> {lvalue}, graph_tool::entropy_args_t) -- 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 7

python: symbol lookup error: libgraph_tool_draw.so: undefined symbol: _ZN5Cairo7ContextC1EP6_cairob
by P-M 25 Jan '17

25 Jan '17

Hi Tiago, Thank you for the help so far. Carrying on the post from gitlab (https://git.skewed.de/count0/graph-tool/issues/367 ) the problem seems to not be solved yet. I have set `export LD_LIBRARY_PATH="-L/home/pmj27/anaconda/lib"` in `~/.bashrc` and `~/.profile`. If I type `echo $LD_LIBRARY_PATH` the shell returns `-L/home/pmj27/anaconda/lib` as I would expect. However, running `graph_draw` still returns the error `python: symbol lookup error: /home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so: undefined symbol: _ZN5Cairo7ContextC1EP6_cairob`. Do you have any other thoughts on what might be going wrong here? As mentioned, it was compiled using `sudo ./configure CXX="g++-5" CXXFLAGS="-std=gnu++14 -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda/bin/python2.7" CAIROMM_LIBS="-L/home/pmj27/anaconda/include/cairomm-1.0/cairomm" --enable-openmp`. 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.

2 5

Efficiently iterating over vertex pairs in graph-tool
by Snehal Shekatkar 24 Jan '17

24 Jan '17

Hello all, I am working on the generation of some random graph model in which probability of having an edge between two given vertices is some complicated function. Hence I cannot use in-built models to generate this graph. Thus, I am using nested for loops to generate it. However, this makes the code extremely slow. Is it possible to iterate over all the pairs of vertices efficiently in graph-tool so that there would be sufficient increase in the speed? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

2 3

Is it possible to save a state and access it later again?
by P-M 23 Jan '17

23 Jan '17

Hi Tiago, I am just about to start some work with the inference module (which looks great by the way!) and was wondering, is it possible for me to store the state class somehow? e.g. if I have minimised my nested block model, can I store the results somehow so that next time I want to work with that same graph again I can skip the minimisation step and just load my past results? Or have I gotten the wrong end of the stick with this? Cheers, 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.

2 1

state.copy(bs=bs, sampling=True) throws error
by Peter Straka 19 Jan '17

19 Jan '17

Dear list, I have a nested, layered state, and would like to do MCMC sampling; but state.copy(bs=bs, sampling=True) throws an error (below)... can this be fixed? Many thanks, Peter Traceback (most recent call last): File "code/model_averaging.py", line 38, in <module> state = state.copy(bs=bs, sampling=True) File "/share/apps/python/gcc6/2.7.12/lib/python2.7/site-packages/graph_tool/inference/nested_blockmodel.py", line 145, in copy **kwargs) File "/share/apps/python/gcc6/2.7.12/lib/python2.7/site-packages/graph_tool/inference/nested_blockmodel.py", line 109, in __init__ bstate = state.get_block_state(b=b, **args) File "/share/apps/python/gcc6/2.7.12/lib/python2.7/site-packages/graph_tool/inference/layered_blockmodel.py", line 532, in get_block_state **kwargs) File "/share/apps/python/gcc6/2.7.12/lib/python2.7/site-packages/graph_tool/inference/layered_blockmodel.py", line 149, in __init__ "layer_entropy"])) File "/share/apps/python/gcc6/2.7.12/lib/python2.7/site-packages/graph_tool/inference/blockmodel.py", line 408, in __init__ str(list(kwargs.keys()))) ValueError: unrecognized keyword arguments: ['copy_bg']

2 2