[R] sparse matrix, rnorm, malloc
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Jun 10 22:42:54 CEST 2006
On Sat, 10 Jun 2006, g l wrote:
> Hi,
>
> I'm Sorry for any cross-posting. I've reviewed the archives and could
> not find an exact answer to my question below.
>
> I'm trying to generate very large sparse matrices (< 1% non-zero
> entries per row). I have a sparse matrix function below which works
> well until the row/col count exceeds 10,000. This is being run on a
> machine with 32G memory:
>
> sparse_matrix <- function(dims,rnd,p) {
> ptm <- proc.time()
> x <- round(rnorm(dims*dims),rnd)
> x[((abs(x) - p) < 0)] <- 0
> y <- matrix(x,nrow=dims,ncol=dims)
> proc.time() - ptm
> }
>
> When trying to generate the matrix around 20,000 rows/cols on a
> machine with 32G of memory, the error message I receive is:
>
> R(335) malloc: *** vm_allocate(size=3200004096) failed (error code=3)
> R(335) malloc: *** error: can't allocate region
> R(335) malloc: *** set a breakpoint in szone_error to debug
> R(335) malloc: *** vm_allocate(size=3200004096) failed (error code=3)
> R(335) malloc: *** error: can't allocate region
> R(335) malloc: *** set a breakpoint in szone_error to debug
> Error: cannot allocate vector of size 3125000 Kb
> Error in round(rnorm(dims * dims), rnd) : unable to find the argument
> 'x' in selecting a method for function 'round'
>
> * Last error line is obvious. Question: on machine w/32G memory, why
> can't it allocate a vector of size 3125000 Kb?
>
> When trying to generate the matrix around 30,000 rows/cols, the error
> message I receive is:
>
> Error in rnorm(dims * dims) : cannot allocate vector of length 900000000
> Error in round(rnorm(dims * dims), rnd) : unable to find the argument
> 'x' in selecting a method for function 'round'
>
> * Last error line is obvious. Question: is this 900000000 bytes?
> kilobytes? This error seems to be specific now to rnorm, but it
> doesn't indicate the length metric (b/Kb/Mb) as it did for 20,000
> rows/cols. Even if this Mb, why can't this be allocated on a machine
> with 32G free memory?
This is a length of 900000000, as it says. Please read ?"Memory-limits"
for the limits in force. (A numeric vector of that length would be over
2^32 bytes and so exceed the address space of a 32-bit executable.)
You have not told us your platform or other basic facts:
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
and had you heeded that request we would have had a lot more to go on.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
More information about the R-help
mailing list