I have been playing around with the inference module from graph-tool a bit and tried to replicate a section of code from the cookbook section. When running gt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10)) I however get an error message.
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)).
Does anybody know what is going wrong here/how I could fix it?
This is the relevant code snippet:
import graph_tool.all as gtimport timeit, osimport cPickle as pickleimport numpy as npg = gt.load_graph('graph_no_multi_reac_type.gt')gt.remove_parallel_edges(g)state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True)# We will first equilibrate the Markov chaingt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10))And this is the error message I get:
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)