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

Tiago de Paula Peixoto tiago at skewed.de
Tue Feb 14 18:27:49 CET 2017


On 14.02.2017 17:20, P-M wrote:
> 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

Please supply the actual graph you used, so this can be investigated.

The git version you tried is more than a month old; do you see this problem
with a current git version?

Since you tried with 2.20dev, I assume you compiled it yourself. What OS are
you using, what GCC version do you have, and are you using sparsehash or not?

Best,
Tiago

-- 
Tiago de Paula Peixoto <tiago at skewed.de>

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