Re: [igraph] memory problem

[Gábor Csárdi]

On Tue, Feb 3, 2009 at 1:12 PM, paolo <address@hidden> wrote:
> Hi,
> still it is weird. It works for centrality measures and not for the shortest
> paths.

Probably they don't store an O(n^2) matrix.

> Also, since we're talking about a sparse matrix, I wouldn't expect
> the algorithm to get all that memory for all those zeros...

Why would it be sparse? This is a matrix that gives the distance from
each vertex to every other vertex. It is not sparse, in fact it only
has zeros in the diagonal. This is a very dense matrix.

Calculate it only for the sources you are interested in.

Gabor

> -----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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-- 
Gabor Csardi <address@hidden>     UNIL DGM