Hi Ross,
It's not obvious how useful memory.profile() is here. I created the
following little experiment to help me understand what
memory.profile() is showing (and to make it easier to see the
changes), but it's left me more confused than enlightened:
m_delta <- function(expr) {
# Evaluate in clean environment to limit effects
e <- new.env(parent = parent.frame())
# Force gc to flush any values no longer attached to names
gc()
old <- memory.profile()
eval(substitute(expr), env = e)
gc()
new <- memory.profile()
report <- cbind(old, new, delta = new - old)
# Only show rows where something changed
report[report[, 3] != 0, ]
}
# Why does this create 3 pairlists, 1 integer and 1 character,
# but no doubles?
m_delta(x <- 1.5)
# No different
m_delta({x <- 1.5})
# Only creates an extra pairlist compared to the previous case
m_delta({x <- 1.5; y <- 2.5})
# Creates 2 pairlists, 1 integer and 1 character even the code
# should have no lasting impact
m_delta(1)
For your original case, you may find it more useful to do memory +
line profiling (e.g. as visualised by
https://github.com/hadley/lineprof) to figure out what's going on.
Hadley
On Fri, Dec 27, 2013 at 1:49 PM, Ross Boylan <r...@biostat.ucsf.edu> wrote:
> I am trying to understand why a function causes my memory use to
> explode. While doing that I noticed that my memory use as reported by
> gc() is growing, but the results of memory.profile() are almost
> unchanged (the count for raw grew by 3). How can the two functions
> produce different results, and what does it mean?
>
> > system.time(r <- Reduce(addResults, bigr[1:10]))
> user system elapsed
> 3.437 0.000 3.444
> > gc()
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 2994756 160.0 4418719 236.0 3587436 191.6
> Vcells 797226672 6082.4 2470056017 18845.1 7340162895 56001.0
> > memory.profile()
> NULL symbol pairlist closure environment promise
> 1 13324 1193588 34602 3000 9754
> language special builtin char logical integer
> 305689 44 637 52237 53954 141713
> double complex character ... any list
> 548076 38 426187 39 0 116692
> expression bytecode externalptr weakref raw S4
> 1 65604 4195 708 735 23935
> > system.time(r <- Reduce(addResults, bigr[1:20]))
> user system elapsed
> 8.432 0.164 10.315 # suspiciously higher than 2* time for 10
> > gc()
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 2994759 160.0 4418719 236.0 3587436 191.6
> !Vcells 828653314 6322.2 2470056017 18845.1 7340162895 56001.0
> > memory.profile()
> NULL symbol pairlist closure environment promise
> 1 13324 1193588 34602 3000 9754
> language special builtin char logical integer
> 305689 44 637 52237 53954 141713
> double complex character ... any list
> 548076 38 426187 39 0 116692
> expression bytecode externalptr weakref raw S4
> 1 65604 4195 708 738 23935
> # by eye, the only change is raw, from 735 to 738.
>
> R 3.0.1 running on Debian GNU/Linux squeeze.
>
> Ross Boylan
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
http://had.co.nz/
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