[graph-tool] Bug in Graph pruning?

Sebastian Weber sebastian.weber at frias.uni-freiburg.de
Tue May 31 09:01:17 CEST 2011


Hi Tiago!

Enclosed is a python script which produces the error. I will send the corresponding data file for the example to your personal address in order not to spam half a megabyte to the list. Moreover, when writing the example I encountered weird problems in the find_vertex function. I compile graph-tool without openmp, but apparently there are some issues here with it. When I use find_vertex, as commented out in the example, then the program crashes with this error:

dyld: lazy symbol binding failed: Symbol not found: _omp_get_num_threads
  Referenced from: /Volumes/Data/sebi/.local/lib/python2.6/site-packages/graph_tool/util/libgraph_tool_util.so
  Expected in: flat namespace

dyld: Symbol not found: _omp_get_num_threads
  Referenced from: /Volumes/Data/sebi/.local/lib/python2.6/site-packages/graph_tool/util/libgraph_tool_util.so
  Expected in: flat namespace

^CTrace/BPT trap

Hence, there seem to be some openmp issues even though I disabled it (or at least did not enable it during compilation). Not using find_vertex, but find_pink does work instead.

Cheers,

Sebastian

Am 31.05.2011 um 00:38 schrieb Tiago de Paula Peixoto:

> On 05/30/2011 04:18 PM, Sebastian Weber wrote:
>> I just discovered a quite strange behavior of graph-tool. I want to
>> keep only the largest component of my network and the following code
>> 
>>    comp = label_largest_component(G)
>>    lc = comp.a == 1
>>    Gv = Graph(GraphView(G, vfilt=lc), prune=True)
>> 
>> simply gives wrong results. It deletes vertices which are in the LC
>> and have comp[v]==1 !!!
> 
> I cannot reproduce this problem. Do you have a concrete (and simple)
> example of where this happens?
> 
> With "prune=True", the filtered vertices are not deleted, but rather
> only the non-filtered vertices are copied. So in order for this to
> somehow fail, there must be something wrong with the filtered graph you
> are trying to copy.
> 
> BTW, why do you use 'lc' as the vfilt parameter of GraphView, instead of
> 'comp' directly?
> 
> Cheers,
> Tiago
> -- 
> Tiago de Paula Peixoto <tiago at skewed.de>
> 
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-- 
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
Albertstr. 19
79104 Freiburg
T.: +49-761-203-97237
Fax:+49-761-203-97334
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