[SciPy-User] MemoryError in scipy.sparse.csgraph.shortest_path

[Giovanni Luca Ciampaglia]

On 05/31/2013 05:54 AM, scipy-user-request at scipy.org wrote:
>> It seems that there are two distinct issues: 1. floyd_warshall() calls 
>> validate_graph with csr_output = False (_shortest_path.pyx:218), causing the 
>> graph to be converted to dense. I believe this a bug. 2. dijkstra creates a 
>> dense distance matrix (_shortest_path.pyx:409). I understand that one cannot 
>> make any assumption about the connectivity of the graph, and thus of the 
>> sparsity of the distance matrix itself; and of course I can get around this 
>> calling dijkstra multiple times with a manageable chunk of indices, and 
>> discarding the values that are equal to inf, but it would be nonetheless nice 
>> if the code tried to do something similar, at least for the cases when one 
>> knows that most of the distances will be inf. 
> Hi Giovanni, sorry no one replied so far. Could you please open an issue
> for this on Github?
>
> Thanks,
> Ralf

Hi Ralf,

done, it's here: https://github.com/scipy/scipy/issues/2526

Do I have to specify assignees?


Best,

-- 
Giovanni Luca Ciampaglia

Postdoctoral fellow
Center for Complex Networks and Systems Research
Indiana University

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✉ gciampag at indiana.edu