[Networkit] NetworKit Digest, Vol 16, Issue 16

Ian ian.wood at anu.edu.au
Tue Mar 3 02:36:03 CET 2015


Before I reply, a question: is there a way to load a graph from a gzip'ed file or from a python file-like-object?


> 
> Hi Ian,
> a segfault should never happen, so we need to do some repair work. However, it?s not clear what causes the error, there are many possibilities along the way. A couple of diagnostics questions:
> 
> - What is the result of properties.size(G) ?
    (265724,17425529)
> - Is G directed or weighted?
    directed, not weighted
> - Is it only ConnectedComponents that fails while other algorithms run properly?
    I've only looked at communities (PLM) and the degree distribution, they work ok.
    I made an undirected version of G, and connected components is working fine on it.
> - Can you verify that the GMLReader reads your input file format correctly, e.g. with a smaller example?
I constructed a smaller graph (with networkx) from a random selection of nodes in my big graph and some of their neighbours, saved as gml, and imported into networkit. properties.overview works fine on this graph.
I also constructed a tiny graph with edges (i,i+1) for i in range(10), and it imports as it should.
The GML files were made with networkx.write_gml(). 

Is there a way I can turn on more verbose debug logging? 

I don't think I mentioned that the networkit version is 3.4.1, installed with pip.

Cheers
Ian
> 
> Chris
> 
> 
> On 27 Feb 2015, at 06:44, Ian <ian.wood at anu.edu.au> wrote:
> 
>> Hi Chris,
>> 
>> I have a software stack running in python 2 that I don't really have time to port. There may be some modules without python 3 support too.
>> 
>> I tried today to install into a virtualenv running python 3.3, but I'm still using Ubuntu 12.04 which only has 3.2 in it's default repositories. It was matplotlib that gave me lots of trouble - it wasn't recognising system installed backends (perhaps because they're compiled against  python 3.2?). I'm giving up on that for now - too much time in that black hole already!  It might be a good idea to add python3 to the requirements list on the "Getting Started" page.. 
>> 
>> I put together a new virtual machine with Ubuntu 14.04 which has the required versions and installed networkit into a virtual env - all good.
>> I now have a problem though. I've a directed graph with some 265k nodes and 17 million edges. 
>> I can read it in ok, but when I do properties.overview(G), I get this:
>> 
>> In [5]: G = graphio.readGraph("netowrk-internal.gml",Format.GML)
>> 
>> In [6]: prop                                    
>> properties  property                            
>> 
>> In [6]: properties.overview(G,showDegreeHistogram=False)
>> INFO:root:[...] calculating properties          
>> INFO:root:[...] determining degree distribution 
>> Value 0 in data. Throwing out 0 values          
>> Calculating best minimal value for power law fit
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:546: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data!=None and not (parameter_range and self.parent_Fit):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:1047: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:598: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:671: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:556: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:1166: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> /home/ubuntu/python-virtual-environments/networkit/lib/python3.4/site-packages/networkit/powerlaw.py:725: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
>>  if data==None and hasattr(self, 'parent_Fit'):
>> INFO:root:[...] detecting communities           
>> INFO:root:[...] performing community detection: PLM
>> <_NetworKit.PLM object at 0x7f34a977cc88>       
>> INFO:root:[...] preparing degree histogram      
>> INFO:root:[...] finding connected components....
>> Segmentation fault   
>> 
>> It may be relevant that it's twitter data, so node id's are python int's, and many are long (ie: I think more than a C long int)?
>> If you give me instructions, I can attempt to get more informative diagnostics..
>> 
>> Cheers
>> Ian
>> 
>> On 20/02/2015, at 10:00 PM, <networkit-request at ira.uni-karlsruhe.de> wrote:
>> 
>>> Message: 3
>>> Date: Fri, 20 Feb 2015 10:08:50 +0100
>>> From: Christian Staudt <christian.staudt at kit.edu>
>>> To: "NetworKit: a toolkit for high-performance network analysis"
>>> 	<networkit at ira.uni-karlsruhe.de>
>>> Subject: Re: [Networkit] pip install fails with "cannot import name
>>> 	DEVNULL"
>>> Message-ID: <66B1DEB7-7E4C-437C-B5B8-07BDE89A7996 at kit.edu>
>>> Content-Type: text/plain; charset="windows-1252"
>>> 
>>> 
>>> On 20 Feb 2015, at 03:15, Ian <ian.wood at anu.edu.au> wrote:
>>> 
>>>> OK, it's proving difficult to install with pip (as opposed to pip3, which I've not tried yet - will it be available to python 2.7 if I install with pip3??)
>>> 
>>> Hi Ian,
>>> it seems like you are trying to install networkit for Python 2.x. However, Python 3.x is required. Support for Python 2 is not something we have currently planned, frankly I do not see the point in backporting. So what are your reasons for wanting to stick with Python 2 rather than upgrading?
>>> 
>>> Best,
>>> Chris

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