I've been investigating and I partially respond myself. I tried the
packages 'bigmemory' and 'ff' and for me the latter did the work I need
pretty straightforward. I create the array in filebacked form with the
function ff, and it seems that the usual R indexing works well. I have yet
to see the limitations, but I hope it helps.
a foo example:
myArr <- ff(NA, dim=rep(904,3), filename="arr.ffd", vmode="double")
myMat <- matrix(1:904^2, ncol=904)
for ( i in 1:904 ) {
myArr[,,i] <- myMat
}
Thanks all,
2012/2/11 Duncan Murdoch <murdoch.dun...@gmail.com>
> On 12-02-10 9:12 AM, Djordje Bajic wrote:
>
>> Hi all,
>>
>> I am trying to fill a 904x904x904 array, but at some point of the loop R
>> states that the 5.5Gb sized vector is too big to allocate. I have looked
>> at
>> packages such as "bigmemory", but I need help to decide which is the best
>> way to store such an object. It would be perfect to store it in this
>> "cube"
>> form (for indexing and computation purpouses). If not possible, maybe the
>> best is to store the 904 matrices separately and read them individually
>> when needed?
>>
>> Never dealed with such a big dataset, so any help will be appreciated
>>
>> (R+ESS, Debian 64bit, 4Gb RAM, 4core)
>>
>
> I'd really recommend getting more RAM, so you can have the whole thing
> loaded in memory. 16 Gb would be nice, but even 8Gb should make a
> substantial difference. It's going to be too big to store as an array
> since arrays have a limit of 2^31-1 entries, but you could store it as a
> list of matrices, e.g.
>
> x <- vector("list", 904)
> for (i in 1:904)
> x[[i]] <- matrix(0, 904,904)
>
> and then refer to entry i,j,k as x[[i]][j,k].
>
> Duncan Murdoch
>
>
>
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