[R] Memory woes

[John D. Barnett]

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.

My first question is, how much memory should this matrix occupy?  Is it
~4000^2 * sizeof(double)?

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?

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?

In case this is relevant, here are my system particulars:

PII, 256M ram + ~500M swap
RedHat 6.1 Linux
R 0.65.1

Thanks in advance for your helpful replies!

-John Barnett


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