You may take a look at the bigmemory package or other which deal with large
memory data in
https://cran.r-project.org/web/views/HighPerformanceComputing.html#large-memory-and-out-of-memory-data
Some extra explanation is in https://stackoverflow.com/a/11127229/997979
Iago
________________________________
De: R-help <r-help-boun...@r-project.org> de part de Eric Berger
<ericjber...@gmail.com>
Enviat el: dimecres, 12 d’abril de 2023 8:38
Per a: Bert Gunter <bgunter.4...@gmail.com>
A/c: R-help <r-help@r-project.org>
Tema: Re: [R] Matrix scalar operation that saves memory?
One possibility might be to use Rcpp.
An R matrix is stored in contiguous memory, which can be considered as a
vector.
Define a C++ function which operates on a vector in place, as in the
following:
library(Rcpp)
cppFunction(
'void subtractConst(NumericVector x, double c) {
for ( int i = 0; i < x.size(); ++i)
x[i] = x[i] - c;
}')
Try this function out on a matrix. Here we define a 5x2 matrix
m <- matrix(150.5 + 1:10, nrow=5)
print(m)
[,1] [,2]
[1,] 151.5 156.5
[2,] 152.5 157.5
[3,] 153.5 158.5
[4,] 154.5 159.5
[5,] 155.5 160.5
Now call the C++ function
subtractConst(m,100.0)
print(m)
[,1] [,2]
[1,] 51.5 56.5
[2,] 52.5 57.5
[3,] 53.5 58.5
[4,] 54.5 59.5
[5,] 55.5 60.5
HTH,
Eric
On Wed, Apr 12, 2023 at 7:34 AM Bert Gunter <bgunter.4...@gmail.com> wrote:
> I doubt that R's basic matrix capabilities can handle this, but have a look
> at the Matrix package, especially if your matrix is some special form.
>
> Bert
>
> On Tue, Apr 11, 2023, 19:21 Shunran Zhang <
> szh...@ngs.gen-info.osaka-u.ac.jp>
> wrote:
>
> > Hi all,
> >
> > I am currently working with a quite large matrix that takes 300G of
> > memory. My computer only has 512G of memory. I would need to do a few
> > arithmetic on it with a scalar value. My current code looks like this:
> >
> > mat <- 100 - mat
> >
> > However such code quickly uses up all of the remaining memory and got
> > the R script killed by OOM killer.
> >
> > Are there any more memory-efficient way of doing such operation?
> >
> > Thanks,
> >
> > S. Zhang
> >
> > [[alternative HTML version deleted]]
> >
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> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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[[alternative HTML version deleted]]
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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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