[R] Memory woes
Prof Brian D Ripley
ripley at stats.ox.ac.uk
Fri Jan 28 17:28:03 CET 2000
On Fri, 28 Jan 2000, John D. Barnett wrote:
> Hello all-
> I'm having some problems with memory consumption under R. I've tried
> increasing the appropriate memory values, but it keeps asking for more;
> I've even upped the heap size to 600M, significantly eating into swap
> (256M real, 500+M swap). So, performance slows to a crawl.
> What I'm trying to do is run isoMDS on a 4000x4000 matrix.
Oops. That is an O(n^4) algorithm in n points. Forget it for more than a
few hundred points.
> My first question is, how much memory should this matrix occupy? Is it
> ~4000^2 * sizeof(double)?
Yes, approximately 128Mb.
> I have an idea about what's going on, but I'm not sure; perhaps someone
> could correct me if this interpretation is wrong. Since R uses
> call-by-value, all data structures are first duplicated, and then handed
> off to the function called. I was getting out of memory errors in
> calling isoMDS; once I got around that, and waited to see what would
> happen next (after about 5 minutes of swapping), I got an error saying
> cmdscale not found. Since isoMDS begins:
> isoMDS <- function(d, y=cmdscale(d, 2), maxit=50, trace=TRUE)
> this means that the whole time I was waiting, was spent in copying d.
> Is this correct?
No. It was also testing for any identical pairs of rows.
> Since the global environment is actually accessible from within
> functions, could I modify this to use call-by-reference? Are there any
> pitfalls I should watch out for?
You could do that (just leave it out from the argument list), and
you could simplify the code, but the .C call would take for ever
(not literally). I suspect you would never get that far (as cmdscale
is also slow: it needs an eigendecomposition, and that is O(n^3)
and by then you would have several versions of your 128Mb matrix around).
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 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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