[R] Large database help
Uwe Ligges
ligges at statistik.uni-dortmund.de
Tue May 16 09:37:38 CEST 2006
Rogerio Porto wrote:
> Hello all.
>
> I have a large .txt file whose variables are fixed-columns,
> ie, variable V1 goes from columns 1 to 7, V2 from 8 to 23 etc.
> This is a 60GB file with 90 variables and 60 million observations.
>
> I'm working with a Pentium 4, 1GB RAM, Windows XP Pro.
> I tried the following code just to see if I could work with 2 variables
> but it seems not possible:
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.2.1 (2005-12-20 r36812)
> ISBN 3-900051-07-0
>
>>gc()
>
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 169011 4.6 350000 9.4 350000 9.4
> Vcells 62418 0.5 786432 6.0 289957 2.3
>
>>memory.limit(size=4090)
>
> NULL
>
>>memory.limit()
>
> [1] 4288675840
>
>>system.time(a<-matrix(runif(1e6),nrow=1))
>
> [1] 0.28 0.02 2.42 NA NA
>
>>gc()
>
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 171344 4.6 350000 9.4 350000 9.4
> Vcells 1063212 8.2 3454398 26.4 4063230 31.0
>
>>rm(a)
>>ls()
>
> character(0)
>
>>system.time(a<-matrix(runif(60e6),nrow=1))
>
> Error: not possible to alocate vector of size 468750 Kb
> Timing stopped at: 7.32 1.95 83.55 NA NA
>
>>memory.limit(size=5000)
>
> Erro em memory.size(size) : .....4GB
>
> So my questions are:
> 1) (newbie) how can I read fixed-columns text files like this?
> 2) is there a way I can analyze (statistics like correlations, cluster etc)
> such a large database neither increasing RAM nor changing to 64bit
> machine but still using R and not using a sample? How?
Use what you are already suggesting in your subject: a database.
Then you can access the variables separately and you have no problems
reading the file.
Even with a real database, if you want to calculate on 60 million
observations (~500Mb) at once, you are near the limit, but only works if
you do not need several variables at once and depends on the methods you
are going to apply.
Uwe Ligges
> Thanks in advance.
>
> Rogerio.
>
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