RE: [igraph] memory problem

[paolo]

Hi,
still it is weird. It works for centrality measures and not for the shortest
paths. Also, since we're talking about a sparse matrix, I wouldn't expect
the algorithm to get all that memory for all those zeros...

-----Original Message-----
From: address@hidden
[mailto:address@hidden On Behalf Of
Gábor Csárdi
Sent: 30 January 2009 11:39
To: Help for igraph users
Subject: Re: [igraph] memory problem

Hi,

On Fri, Jan 30, 2009 at 12:30 PM, paolo <address@hidden> wrote:
> Hi,
>
> I'm trying to compute the shortest path for a weighted network with around
> 170000 vertices and 201000 edges. This is what happens:
>
>
>
>> s<-shortest.paths(g,weights = NULL)
>
> Error in shortest.paths(g, weights = NULL) :
>
>   At vector.pmt:408 : cannot reserve space for vector, Out of memory
>
>
>
> I run Igraph on R, windows XP, with an intel core 2, CPU T7400 at 2.16GHz,
> with 2GB of RAM.
>
> I attach the network I'm trying to work on.
>
> Do you think there is any chance I can sort it out?

It is not very hard "solve" this mystery, you have 170,000 vertices,
the result of this computation is a 170,000x170,000 matrix of 8-byte
doubles, to store this you need about 231.2 Gbytes of memory.

You can do the calculation for a subset of vertices if you give the
'v' argument.

Gabor

> My best regards
>
> Paolo
>
>
>
> Paolo Masucci | CASA | University College London | 1-19 Torrington Place
> London WC1E 6BT UK | Tel 44 207 679 1255 |
>
> email: address@hidden | web: www.casa.ucl.ac.uk
>
>
>
> _______________________________________________
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>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM


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