[Networkit] Reading graph segfaults

Lars Beckmann lars.beckmann at gmail.com
Thu Apr 24 16:34:19 CEST 2014


Hi Christian,

yes, I did a rebuild after switching to Dev. To rebuild, I ran "sudo scons
--optimize=O --target=Core", which worked fine as far as I can see. Only
when I try to run the python import statement, I get that error.

Any other ideas?

Best,

Lars


On Thu, Apr 24, 2014 at 4:26 PM, Staudt, Christian (ITI) <
christian.staudt at kit.edu> wrote:

> Hi Lars,
> I cannot reproduce your error, „from NetworKit import *“ works fine for me.
>
> Are you sure the package is properly built? Did you rebuild when you
> switched branches? That could be the reason why PageRank is not there.
>
> Best,
> Christian
>
> Am 24.04.2014 um 16:18 schrieb Lars Beckmann <lars.beckmann at gmail.com>:
>
> Hi Christian,
>
> thanks for the info! I pulled from the repo and updated to the dev branch.
> I then built the core, which worked without errors. When I then tried to do
> "from NetworKit import *", I get this error message:
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/home/adminuser/Utilities/NetworKit/src/python/NetworKit.py", line
> 24, in <module> import centrality
> File "/home/adminuser/Utilities/NetworKit/src/python/centrality.py", line
> 1, in <module> from _NetworKit import Betweenness, PageRank,
> EigenvectorCentrality, DegreeCentrality, ApproxBetweenness
>  ImportError: cannot import name PageRank
>
> When I switched back to the default branch, rebuilt and ran the statement
> again, I got no errors. But ApproxBetweenness is only in the Dev branch as
> far as I could see. I am not a Python expert, so maybe there is an obvious
> solution to only import ApproxBetweenness. For now I would be happy to test
> that part (PageRank is interesting too, but maybe later). Or are we doing
> something completely wrong here?
>
> Best,
>
> Lars
>
>
> On Tue, Apr 22, 2014 at 1:24 PM, Staudt, Christian (ITI) <
> christian.staudt at kit.edu> wrote:
>
>> Hi Lars,
>> in addition to the paper mentioned by Henning (
>> http://arxiv.org/abs/1403.3005), there a two main sources  for
>> documentation on NetworKit’s classes and functions:
>>
>> a) the user guide in the form of an IPython Notebook:
>> Doc/Notebooks/NetworKit_UserGuide.ipynb
>> b) the Python docstrings for classes and functions, as well as Doxygen
>> comments in the C++ source code
>>
>> I admit that both sources are not in perfect shape, so please inform us
>> if and maybe how they could be improved.
>>
>> Especially for centrality.ApproxBetweenness, which is a very recent
>> addition, we are interested in your practical experiences, e.g. Did it work
>> for your data? How long did it take? Which parameters did you chose for
>> your purposes? etc.
>>
>> Kind regards
>> Christian
>>
>> christian.staudt at kit.edu
>> http://parco.iti.kit.edu/staudt/index-en.shtml
>> Institut of Theoretical Computer Science - Parallel Computing Group
>> Building 50.34 Room 249
>> Karlsruhe Institute of Technology (KIT)
>>
>>
>>
>>
>>
>> Am 22.04.2014 um 12:54 schrieb Lars Beckmann <lars.beckmann at gmail.com>:
>>
>> Hi Henning,
>>
>> thanks for the quick reply, that fixed the issue.
>>
>> Christian said that there is an approximation algorithm for betweenness
>> centrality in the dev-branch. Is there an overview for all the available
>> algorithms and their usage? In particular we are interested in centrality
>> measures for very large graphs (millions of nodes, (hundreds of) millions
>> of edges). If you could point me to docs or any other resource that shows
>> the usage of these algorithms, that would be great. Note: I did go trough
>> the doc folder in the repo, but maybe there is more that I haven't found
>> yet?
>>
>> Thanks in advance,
>>
>> Lars
>>
>>
>> On Fri, Apr 18, 2014 at 5:49 PM, Henning Meyerhenke <meyerhenke at kit.edu>wrote:
>>
>>> Dear Lars,
>>>
>>> Thanks for your request. The reason for the error is the input graph's
>>> slight, yet important deviation from the input format requirements. The
>>> Metis format requires graphs to be 1-indexed, i.e. vertex indices start
>>> with 1, not 0.
>>>
>>> The unfulfilled assertion happens when an edge with index 0 occurs. Then
>>> NetworKit's range check fails.
>>>
>>> Could you please change your data set according to the format and try
>>> again?
>>>
>>> Thanks,
>>> Henning
>>>
>>>
>>> Am 18.04.14 15:03, schrieb Lars Beckmann:
>>>
>>>  Hi,
>>>>
>>>> we are trying to use NetworKit to compute centrality measures, but
>>>> NetworKit segfaults when we try to read the graph. We are using a clean
>>>> VM with Ubuntu 13.10
>>>> (http://virtualboximages.com/Ubuntu+13.10+amd64+VirtualBox+
>>>> VDI+Virtual+Appliance)
>>>> where we installed the prerequisites mentioned in the NetworKit readme.
>>>> We successfully built NetworKit on the VM, but when we try to read our
>>>> graph using: G = graphio.METISGraphReader().read("xxx.graph") NetworKit
>>>> segfaults. We have built NetworKit without debug flags, but we can do
>>>> so, if that is important for the devs to help us out.
>>>>
>>>> You can find the graph in question here:
>>>> https://drive.google.com/file/d/0B7vRIovbLojkSHpTUy1hR3dFRHM/
>>>> edit?usp=sharing
>>>>
>>>> Thanks for your help,
>>>>
>>>> Lars
>>>>
>>>> --
>>>> Lars Beckmann
>>>>
>>>> Uhlenstraße 10
>>>> 33098 Paderborn
>>>> Germany
>>>>
>>>> Cell (D2): +49 (0) 178 59 69 150
>>>> Phone: +49 (0) 89 380 123 90
>>>> Fax: +49 (0) 180 102 113 4628
>>>>
>>>
>>> --
>>>
>>> =======================================================
>>> Karlsruhe Institute of Technology (KIT)
>>> Institute of Theoretical Informatics (ITI)
>>>
>>> Juniorprof. Dr. Henning Meyerhenke
>>> Theoret. Informatics / Parallel Computing
>>>
>>> Phone: +49-721-608-41876
>>> Web: http://parco.iti.kit.edu/henningm/
>>>
>>> KIT - University of the State of Baden-Wuerttemberg and
>>> National Research Center of the Helmholtz Association
>>> =======================================================
>>>
>>>
>>
>>
>> --
>> Lars Beckmann
>>
>> Uhlenstraße 10
>> 33098 Paderborn
>> Germany
>>
>> Cell (D2): +49 (0) 178 59 69 150
>> Phone: +49 (0) 89 380 123 90
>> Fax: +49 (0) 180 102 113 4628
>>  <ATT00001.c>
>>
>>
>>
>> _______________________________________________
>> NetworKit mailing list
>> NetworKit at ira.uni-karlsruhe.de
>> https://lists.ira.uni-karlsruhe.de/mailman/listinfo/networkit
>>
>>
>
>
> --
> Lars Beckmann
>
> Uhlenstraße 10
> 33098 Paderborn
> Germany
>
> Cell (D2): +49 (0) 178 59 69 150
> Phone: +49 (0) 89 380 123 90
> Fax: +49 (0) 180 102 113 4628
>
>
>


-- 
Lars Beckmann

Uhlenstraße 10
33098 Paderborn
Germany

Cell (D2): +49 (0) 178 59 69 150
Phone: +49 (0) 89 380 123 90
Fax: +49 (0) 180 102 113 4628
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