[graph-tool] Inference - Aborted (core dumped)

P-M pmj27 at cam.ac.uk
Tue Feb 21 13:38:45 CET 2017


Hello Tiago,

I have been running a piece of code to give me some idea how long it takes
me to calculate edge likelihoods as I add vertices and edges to my network.
This works for a while and then it all crashes with a rather nasty looking
error message. The code is very similar to what I have posted  here
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Questions-about-output-of-quot-history-quot-of-graph-tool-inference-mcmc-equilibrate-td4027027.html#a4027051>  
so I won't paste it here again in the interest of brevity, though the entire
script can be found here ( edge_prediction_stats.py
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4027054/edge_prediction_stats.py>  
). When my script gets to a certain point in the loop it crashes with a long
error message. (I have observed this when the code reaches the filtered
network corresponding to pub_year=1870 and pub_year=1880). I presume this
appears to happen when evaluating `state =
gt.minimize_nested_blockmodel_dl(g, deg_corr=True)` as far as I can tell by
the screen output. The error message that I then get is posted below. Is
this caused by an issue in graph-tool? 

I am running Ubuntu 16.04, running gcc -v returns gcc version 4.8.5 (GCC)
though GCC 5.4.0-6ubuntu1~16.04.4 is also installed and my graph-tool
version is 2.20dev (commit 01432d60, Sun Jan 15 19:54:52 2017 +0000).

*** Error in `python': double free or corruption (out): 0x00000000033db2c0
***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7ff250de37e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7ff250debe0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7ff250def98c]
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so(+0x1bf83b1)[0x7ff2405333b1]
/usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x2547c)[0x7ff23e4eb47c]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0xae435)[0x7ff251b10435]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0x8ecab)[0x7ff251af0cab]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0xae4f1)[0x7ff251b104f1]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0x8ecab)[0x7ff251af0cab]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0xae4f1)[0x7ff251b104f1]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0x7f08f)[0x7ff251ae108f]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0x8ecab)[0x7ff251af0cab]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0xae4f1)[0x7ff251b104f1]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(+0x8cbe7)[0x7ff251aeebe7]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyDict_SetItem+0x8c)[0x7ff251af203c]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6ae0)[0x7ff251b5d010]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7ff251b5fa2e]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7ff251b5fb42]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xb0)[0x7ff251b80050]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xef)[0x7ff251b8022f]
/home/pmj27/anaconda/bin/../lib/libpython2.7.so.1.0(Py_Main+0xca4)[0x7ff251b95b74]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff250d8c830]
python[0x400649]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:11 87037196                          
/home/pmj27/anaconda/bin/python2.7
00600000-00601000 rw-p 00000000 08:11 87037196                          
/home/pmj27/anaconda/bin/python2.7
00f8f000-3110f000 rw-p 00000000 00:00 0                                 
[heap]
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/home/pmj27/anaconda/lib/libsqlite3.so.0.8.6
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/home/pmj27/anaconda/lib/libsqlite3.so.0.8.6
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/home/pmj27/anaconda/lib/python2.7/lib-dynload/resource.so
7ff22d468000-7ff22d469000 rw-p 00002000 08:11 111289509                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/resource.so
7ff22d469000-7ff22d46d000 r-xp 00000000 08:11 111289514                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/termios.so
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7ff22e7d0000-7ff22ecd0000 rw-p 00000000 00:00 0
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/home/pmj27/anaconda/lib/python2.7/site-packages/matplotlib/ft2font.so
7ff22eee2000-7ff22eee4000 rw-p 00012000 08:11 90316376                  
/home/pmj27/anaconda/lib/python2.7/site-packages/matplotlib/ft2font.so
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7ff22f024000-7ff22f053000 r-xp 00000000 08:11 90316177                  
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/home/pmj27/anaconda/lib/python2.7/site-packages/matplotlib/_path.so
7ff22f252000-7ff22f254000 rw-p 0002e000 08:11 90316177                  
/home/pmj27/anaconda/lib/python2.7/site-packages/matplotlib/_path.so
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7ff22f65e000-7ff22f65f000 rw-p 00001000 08:11 111289456                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/_bisect.so
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/home/pmj27/anaconda/lib/python2.7/lib-dynload/_ssl.so
7ff22fbb3000-7ff22fbb7000 rw-p 00013000 08:11 111289483                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/_ssl.so
7ff22fbb7000-7ff22fbc5000 r-xp 00000000 08:11 111289481                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/_socket.so
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/home/pmj27/anaconda/lib/python2.7/lib-dynload/_socket.so
7ff22fdc5000-7ff22fdca000 rw-p 0000e000 08:11 111289481                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/_socket.so
7ff22fdca000-7ff22feca000 rw-p 00000000 00:00 0
7ff22feca000-7ff22fece000 r-xp 00000000 08:11 111289510                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/select.so
7ff22fece000-7ff2300ce000 ---p 00004000 08:11 111289510                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/select.so
7ff2300ce000-7ff2300d0000 rw-p 00004000 08:11 111289510                 
/home/pmj27/anaconda/lib/python2.7/lib-dynload/select.so
7ff2300d0000-7ff230190000 rw-p 00000000 00:00 0
7ff230190000-7ff230192000 r-xp 00000000 08:01 5898446                   
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/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7ff230392000-7ff230393000 r--p 00002000 08:01 5898446                   
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7ff230393000-7ff230394000 rw-p 00003000 08:01 5898446                   
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7ff230394000-7ff2303b8000 r-xp 00000000 08:11 87821207                  
/home/pmj27/anaconda/lib/libxcb.so.1.1.0
7ff2303b8000-7ff2305b7000 ---p 00024000 08:11 87821207                  
/home/pmj27/anaconda/lib/libxcb.so.1.1.0
7ff2305b7000-7ff2305b8000 rw-p 00023000 08:11 87821207                  
/home/pmj27/anaconda/lib/libxcb.so.1.1.0
7ff2305b8000-7ff2306a6000 r-xp 00000000 08:11 86776648                  
/home/pmj27/anaconda/lib/libiconv.so.2.5.1
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/home/pmj27/anaconda/lib/libiconv.so.2.5.1
7ff2308a5000-7ff2308a7000 rw-p 000ed000 08:11 86776648                  
/home/pmj27/anaconda/lib/libiconv.so.2.5.1
7ff2308a7000-7ff2309f7000 r-xp 00000000 08:11 87949924                  
/home/pmj27/anaconda/lib/libxml2.so.2.9.2
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/home/pmj27/anaconda/lib/libxml2.so.2.9.2
7ff230bf6000-7ff230c00000 rw-p 0014f000 08:11 87949924                  
/home/pmj27/anaconda/lib/libxml2.so.2.9.2
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/usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
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/usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
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/usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7ff230e12000-7ff230e13000 rw-p 00011000 08:01 5907443                   
/usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
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/usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
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/usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
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/usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7ff231149000-7ff23114d000 rw-p 00136000 08:01 5907424                   
/usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7ff23114d000-7ff231156000 r-xp 00000000 08:01 5901237                   
/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
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/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
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/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7ff231356000-7ff231357000 rw-p 00009000 08:01 5901237                   
/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
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/home/pmj27/anaconda/lib/libpng16.so.16.28.0
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/home/pmj27/anaconda/lib/libpng16.so.16.28.0
7ff231596000-7ff231597000 rw-p 0003f000 08:11 87561104                  
/home/pmj27/anaconda/lib/libpng16.so.16.28.0
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/home/pmj27/anaconda/lib/libfreetype.so.6.11.4
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/home/pmj27/anaconda/lib/libfreetype.so.6.11.4
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/home/pmj27/anaconda/lib/libfreetype.so.6.11.4
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/home/pmj27/anaconda/lib/libfontconfig.so.1.9.2
7ff23186d000-7ff231a6d000 ---p 0003d000 08:11 86776705                  
/home/pmj27/anaconda/lib/libfontconfig.so.1.9.2
7ff231a6d000-7ff231a73000 rw-p 0003d000 08:11 86776705                  
/home/pmj27/anaconda/lib/libfontconfig.so.1.9.2
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/home/pmj27/anaconda/lib/libpixman-1.so.0.34.0
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/home/pmj27/anaconda/lib/libpixman-1.so.0.34.0
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/home/pmj27/anaconda/lib/libpixman-1.so.0.34.0
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/home/pmj27/anaconda/lib/libcairo.so.2.11400.8
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/home/pmj27/anaconda/lib/libcairo.so.2.11400.8
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/home/pmj27/anaconda/lib/libcairo.so.2.11400.8
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7ff232064000-7ff232078000 r-xp 00000000 08:11 115085801                 
/home/pmj27/anaconda/lib/python2.7/site-packages/cairo/_cairo.so
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/home/pmj27/anaconda/lib/python2.7/site-packages/cairo/_cairo.so
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/home/pmj27/anaconda/lib/python2.7/site-packages/cairo/_cairo.so
7ff23227d000-7ff2329da000 r-xp 00000000 08:11 88219624                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.so
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/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.so
7ff232bd9000-7ff232bdd000 r--p 0075c000 08:11 88219624                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.so
7ff232bdd000-7ff232be1000 rw-p 00760000 08:11 88219624                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.so
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/home/pmj27/anaconda/lib/libgmp.so.10.2.0
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/home/pmj27/anaconda/lib/libgmp.so.10.2.0
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/home/pmj27/anaconda/lib/libgmp.so.10.2.0
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/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.so
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/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.so
7ff234259000-7ff23425e000 r--p 011dd000 08:11 88740332                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.so
7ff23425e000-7ff234264000 rw-p 011e2000 08:11 88740332                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.so
7ff234264000-7ff2342a5000 rw-p 00000000 00:00 0
7ff2342a5000-7ff2349b9000 r-xp 00000000 08:11 88477126                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.so
7ff2349b9000-7ff234bb9000 ---p 00714000 08:11 88477126                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.so
7ff234bb9000-7ff234bbb000 r--p 00714000 08:11 88477126                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.so
7ff234bbb000-7ff234bbe000 rw-p 00716000 08:11 88477126                  
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.so
7ff234bbe000-7ff234d7b000 r-xp 00000000 08:11 115086279                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.so
7ff234d7b000-7ff234f7a000 ---p 001bd000 08:11 115086279                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.so
7ff234f7a000-7ff234f7d000 r--p 001bc000 08:11 115086279                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.so
7ff234f7d000-7ff234f7f000 rw-p 001bf000 08:11 115086279                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.so
7ff234f7f000-7ff2388d3000 r-xp 00000000 08:11 115086288                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.so
7ff2388d3000-7ff238ad2000 ---p 03954000 08:11 115086288                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.so
7ff238ad2000-7ff238ada000 r--p 03953000 08:11 115086288                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.so
7ff238ada000-7ff238b05000 rw-p 0395b000 08:11 115086288                 
/home/pmj27/anaconda/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.so
7ff238b05000-7ff238b06000 rw-p 00000000 00:00 0 Aborted (core dumped)



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