[graph-tool] mcmc_equilibrate - Segmentation fault (core dumped)

P-M pmj27 at cam.ac.uk
Tue Feb 14 18:20:41 CET 2017


I am trying to run the following snippet of code:

    import graph_tool.all as gt
    import timeit, os
    import cPickle as pickle
    import numpy as np

    g = gt.load_graph('graph_no_multi_reac_type.gt')
    gt.remove_parallel_edges(g)

    print 'minimising state'
    start = timeit.default_timer()
    state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True,verbose=False)
    duration = timeit.default_timer()-start
    print 'duration: ', duration

    state = state.copy(sampling=True)
    with open('state_n_dc.pkl','wb') as state_pkl:
        pickle.dump(state,state_pkl,-1)
    print 'equilibrating Markov chain'
    start = timeit.default_timer()
    mcmc_args = {}
    mcmc_args=dict(parallel = True,niter=10)
    history = gt.mcmc_equilibrate(state, wait=1000,
history=True,mcmc_args=mcmc_args)
    duration = timeit.default_timer()-start
    print 'duration: ', duration
    with open('history1.pkl','wb') as his1_pkl:
        pickle.dump(history,his1_pkl,-1)

On the attached graph ( graph_no_multi_reac_type.gt
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4027034/graph_no_multi_reac_type.gt>  
). I, however, get an error message stating "Segmentation fault (core
dumped)". To be precise my screen output is:

    minimising state
    duration:  991.349531889
    equilibrating Markov chain
    Segmentation fault (core dumped)

So the error seems to arise during `history = gt.mcmc_equilibrate(state,
wait=1000, history=True,mcmc_args=mcmc_args)`. Why might that be?

I have observed the issue both with  `2.20dev (commit 01432d60, Sun Jan 15
19:54:52 2017 +0000)` and `2.20 (commit f6ef9990, Fri Jan 27 16:40:08 2017
+0000)`.

Best,

Philipp



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