Re: [igraph] problem with large graph

[Gábor Csárdi]

Uri, I think there is something in your data frame that igraph
misinterprets. It might be an NA value somewhere. You could try to
find which line makes igraph fail and then remove/repair it. If you
are stuck, you can send me the data frame in private and I can have a
look.

Best,
Gabor

On Mon, Nov 2, 2009 at 8:32 PM, Tamas Nepusz <address@hidden> wrote:
> Dear Uri,
>
> I'm not an R expert (I mostly use igraph from C or Python), so that's why I
> didn't answer your message so far. The size of the graph you are working
> with (215K nodes, 3M edges) should be no problem for igraph's core, at least
> when it has to store the edges only (without any additional metadata). E.g.,
> doing the following works for me in R (version 2.8.1 on openSuSE 11.1 -- I
> know that this R version is outdated, but this is the default in openSuSE):
>
>> xs <- floor(runif(3000000)*215000)
>> ys <- floor(runif(3000000)*215000)
>> df <- data.frame(xs=xs, ys=ys)
>> g <- graph.data.frame(df)
>> ecount(g)
> [1] 3e+06
>> vcount(g)
> [1] 215000
>> dd <- degree.distribution(g)
>  [1] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
>  [6] 0.000000e+00 0.000000e+00 0.000000e+00 9.302326e-06 2.325581e-05
> [...lines omitted here...]
> [56] 4.651163e-06 0.000000e+00 0.000000e+00 4.651163e-06
>
> However, it could have happened that the edge data together with the
> metadata attached to each edge is too large for R or igraph itself. (Note
> that there is a point when the whole graph is stored twice in the memory,
> once as a data frame, once as an igraph graph, which contains a copy for
> each edge attribute). So, I would first try to construct an igraph graph
> without the attached attributes, i.e. create a data frame with only
> profile_id_a and profile_id_b and check if it works or not. If it works, try
> adding the attributes back to the data frame one by one and find where the
> whole process breaks down. I'm not familiar with R's internal details, so it
> could also have happened that you are hitting an internal limit somewhere;
> maybe Gabor can tell more about this.
>
> --
> Tamas
>
>
>
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>



-- 
Gabor Csardi <address@hidden>     UNIL DGM