Re: [igraph] Inconsistency problems with large 19 million edges graph (proper email)

[Stefano Scerra]

Thank you so much, Tamas. By using Read_Edgelist the expected ids were returned.

Happy Easter, btw,

Bye,

S.

2015-04-05 21:59 GMT+02:00 Tamas Nepusz <address@hidden>:

Hi,

I'm pretty sure that the identifiers that you use in your graph are stored in
the "name" vertex attribute and the integer IDs in igraph are assigned
arbitrarily (since both Graph.Read_Ncol and Graph.TupleList accepts arbitrary
names as vertex identifiers, not only integers). Since the vertex IDs in your
file seem to be integers from zero to |V|-1, use Graph.Read_Edgelist -- this
will use the integer IDs from your file as is, and the edge lookups by ID will
behave as expected.

T.

On 04/05, Stefano Scerra wrote:
> (Sorry for accidentally double posting)
> Hello,
> I'm having a really strange problem with the library and I was hoping to
> get some advice.
>
> After loading a large 19 million edges graph, the library returns an
> inconsistent edge list.
> More precisely, nonexistent edges appear in the graph's edge sequence.
>
> I try to load the graph in two different ways, by using Graph.Read_Ncol,
> and by manually reading the edgelist and then using Graph.TupleList. In
> both cases, iterating on the graph's edge sequence (the es attribute)
> yields inconsistent results: for instance, the nonexisting edge 10->11 is
> returned.
>
> I'm using igraph 0.7.1-4 on Python 3.4.3 64 bit on Windows 7 SP1 64 bit
> Link to the graph:
> https://drive.google.com/file/d/0B0afrBfsijreOS1BZkVfdE10TlE/view?usp=sharing
>
> Here's the code:
>
> from igraph import Graph
> import csv
> import timeit
>
> def create_graph(file_graph):
>     # load graph using Graph.Read_Ncol
>     with open(file_graph, "r") as in_file:
>         g = Graph.Read_Ncol(in_file, weights=False, directed=True)
>         return g
>
> def create_graph2(file_graph):
>     # load graph using Graph.TupleList
>     edges = []
>     with open(file_graph, "r") as in_file:
>         reader = csv.reader(in_file, delimiter=" ")
>         i = 0
>         for row in reader:
>             if row:
>                 edges.append([int(row[0]), int(row[1])])
>                 i += 1
>                 if i % 100000 == 0: print(i)
>     return Graph.TupleList(edges=edges, directed=True)
>
>
> def generate_weighted_graph(input, output):
>     g = create_graph2(input)
>     print("ecount:", g.ecount(), "vcount:", g.vcount())
>     with open(output, "w") as output_file:
>         writer = csv.writer(output_file, delimiter=" ")
>         for e in g.es:
>             i, j = e.source, e.target
>             writer.writerow([i, j])
>
> if __name__ == "__main__":
>     generate_weighted_graph("C:/datasets/network",
> "C:/datasets/network_weighted")
>
>
> Could this possibly be a bug?
> Any help would be appreciated, thank you!
> Stefano

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--
T.

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