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

[Ralf Gommers]

On Fri, May 31, 2013 at 4:57 PM, Giovanni Luca Ciampaglia <
glciampagl at gmail.com> wrote:

> 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
>

Thanks.


> Do I have to specify assignees?
>

Not needed (and I don't think you can without commit rights). We label the
issues and perhaps ping people we know are interested, but don't assign
issues to others. Every committer is welcome to  assign issues to him/her
self though.

Ralf



>
> Best,
>
> --
> Giovanni Luca Ciampaglia
>
> Postdoctoral fellow
> Center for Complex Networks and Systems Research
> Indiana University
>
> ✎ 910 E 10th St ∙ Bloomington ∙ IN 47408
> ☞ http://cnets.indiana.edu/
> ✉ gciampag at indiana.edu
>
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