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Re: [igraph] Out of memory with Graph.Read_Edgelist()

From: Håvard Wahl Kongsgård
Subject: Re: [igraph] Out of memory with Graph.Read_Edgelist()
Date: Mon, 11 Jul 2011 13:42:50 +0200

Thanks, the graph have non-continuous ID's so that is most likely the problem.

If I convert the graph to GraphML or manually read the graph into
igraph, will that solve the problem?


On Mon, Jul 11, 2011 at 1:33 PM, Tamas Nepusz <address@hidden> wrote:
> This is indeed strange, but one thing that may cause this is when your
> numeric edge IDs are not continuous. For instance, if you have only two
> vertices, but one has ID 100000000 and the other one has ID 199999999,
> igraph will try to create a graph with 200 million vertices as the edge IDs
> must always start from zero and be continuous. If your edge IDs are numeric
> but non-continuous, you may want to consider using the NCOL format instead,
> which is basically a "symbolic" edge list where the edge IDs in the file may
> be arbitrary numbers or strings, and they will be assigned to the "name"
> vertex attribute.
> --
> Tamas
> On 07/11/2011 01:27 PM, Håvard Wahl Kongsgård wrote:
>> Hi, when I attempt to read a small edge list (20 000 nodes and 20 000
>> edges) with the python function Graph.Read_Edgelist(),
>> I get this error
>> MemoryError: Error at vector.pmt:409: cannot reserve space for vector,
>> Out of memory
>> It's strange since  Python does use any memory.
>> System: Ubuntu 10
>> Ram 8GB
>> Swap 8GB
>> latest version of igraph from source
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