> -----Original Message-----
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf
> Of Drew Tyre
> Sent: Thursday, April 05, 2012 8:35 AM
> To: Ramiro Barrantes
> Cc: r-help@r-project.org
> Subject: Re: [R] reclaiming lost memory in R
>
> Ramiro
>
> I think the problem is the loop - R doesn't release memory allocated inside
> an expression until the expression completes. A for loop is an expression,
> so it duplicates fit and dataset on every iteration.
The above explanation is not true.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> An alternative
> approach that I have found successful in similar circumstances is to use
> sapply(), like this
>
> fits <- list()
> sapply(1:N,function(i){
> dataset <- generateDataset(i)
> fit[[i]] <- try( memoryHogFunction(dataset, otherParameters))
> })
>
> I'm assuming above that you want to save the result of memoryHogFunction
> from each iteration.
>
> hth
> Drew
> On Thu, Apr 5, 2012 at 8:35 AM, Ramiro Barrantes <
> ram...@precisionbioassay.com> wrote:
>
> > Dear list,
> >
> > I am trying to reclaim what I think is lost memory in R, I have been using
> > gc(), rm() and also using Rprof to figure out where all the memory is going
> > but I might be missing something.
> >
> > I have the following situation
> >
> > basic loop which calls memoryHogFunction:
> >
> > for i in (1:N) {
> > dataset <- generateDataset(i)
> > fit <- try( memoryHogFunction(dataset, otherParameters))
> > }
> >
> > and within
> >
> > memoryHogFunction <- function(dataset, params){
> >
> > fit <- try(nlme(someinitialValues)
> > ...
> > fit <- try(updatenlme(otherInitialValues)
> > ...
> > fit <- try(updatenlme(otherInitialValues)
> > ...
> > ret <- fit ( and other things)
> > return a result "ret"
> > }
> >
> > The problem is that, memoryHogFunction uses a lot of memory, and at the
> > end returns a result (which is not big) but the memory used by the
> > computation seems to be still occupied. The original loop continues, but
> > the memory used by the program grows and grows after each call to
> > memoryHogFunction.
> >
> > I have been trying to do gc() after each run in the loop, and have even
> > done:
> >
> > in memoryHogFunction()
> > ...
> > ret <- fit ( and other things)
> > rm(list=ls()[-match("ret",ls())])
> > return a result "ret"
> > }
> >
> > ???
> >
> > A typical results from gc() after each loop iteration says:
> > used (Mb) gc trigger (Mb) max used (Mb)
> > Ncells 326953 17.5 597831 32.0 597831 32.0
> > Vcells 1645892 12.6 3048985 23.3 3048985 23.3
> >
> > Which doesn't reflect that 340mb (and 400+mb in virtual memory) that are
> > being used right now.
> >
> > Even when I do:
> >
> > print(sapply(ls(all.names=TRUE), function(x) object.size(get(x))))
> >
> > the largest object is 8179808, which is what it should be.
> >
> > THe only thing that looked suspicious was the following within Rprof (with
> > memory=stats option), the tot.duplications might be a problem???:
> >
> > index: "with":"with.default"
> > vsize.small max.vsize.small vsize.large max.vsize.large
> > 30841 63378 20642 660787
> > nodes max.nodes duplications tot.duplications
> > 3446132 8115016 12395 61431787
> > samples
> > 4956
> >
> > Any suggestions? Is it something about the use of loops in R? Is it
> > maybe the try's???
> >
> > Thanks in advance for any help,
> >
> > Ramiro
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Drew Tyre
>
> School of Natural Resources
> University of Nebraska-Lincoln
> 416 Hardin Hall, East Campus
> 3310 Holdrege Street
> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
> fax: +1 402 472 2946
> email: aty...@unl.edu
> http://snr.unl.edu/tyre
> http://aminpractice.blogspot.com
> http://www.flickr.com/photos/atiretoo
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
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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.
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