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

From: Tamas Nepusz
Subject: Re: [igraph] Out of memory with Graph.Read_Edgelist()
Date: Mon, 11 Jul 2011 13:33:19 +0200
User-agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv: Gecko/20110516 Lightning/1.0b2 Thunderbird/3.1.10

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.


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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