Memory problems in R -


here phenomenon happens often. try manipulate sort of big data, example

a <- matrix( rnorm( 1e4 * 200 ), ncol= 1e4 ) gr <- factor( rep( 1:2, each= 100 ) ) l <- lm( ~ gr ) covs <- estvar( l ) cors <- cov2cor( covs )

quite often, following error reported: error: cannot allocate vector of size 509.5 mb

fine. remove variables don't need more , call garbage collector:

rm( a, l ) gc( true )

however, error persists. save r , start again. , -- miracle happens: memory available. why? if there not enough memory r allocate before, there enough now, changed? can force r somehow clean without saving data disk , waiting until loads them again? don't it.

my sessioninfo():

> sessioninfo() r version 3.0.1 (2013-05-16) platform: i486-pc-linux-gnu (32-bit)  locale:  [1] lc_ctype=en_us.utf8       lc_numeric=c              lc_time=en_us.utf8        lc_collate=en_us.utf8     lc_monetary=en_us.utf8     [6] lc_messages=en_us.utf8    lc_paper=c                lc_name=c                 lc_address=c              lc_telephone=c            [11] lc_measurement=en_us.utf8 lc_identification=c        attached base packages: [1] graphics  utils     datasets  grdevices stats     methods   base

p.s.: system appears have plenty of unused memory left, reported free. top reports r process (before error) using ~ 2gb out of 8, , there still plenty more left.

install , use 64-bit r take advantage of more ram. ?memory-limits:

unix
address-space limit system-specific: 32-bit oses imposes limit of no more 4gb: 3gb. running 32-bit executables on 64-bit os have similar limits: 64-bit executables have infinite system-specific limit (e.g. 128tb linux on x86_64 cpus).


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