[R] reclaiming lost memory in R

[Ramiro Barrantes]

Thank you for your feedback.

I think the problem is that, when nlme runs, it "hangs" when iterating.  I have a timeout of 5 minutes so that is how I get it to stop on the few cases where it goes over.  However, I think the memory doesn't get "cleared up" properly.

Please let me know if you have any other suggestions or clues.

Ramiro
________________________________________
From: William Dunlap [wdunlap at tibco.com]
Sent: Thursday, April 05, 2012 9:21 PM
To: Drew Tyre; Ramiro Barrantes
Cc: r-help at r-project.org
Subject: RE: [R] reclaiming lost memory in R

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
> Of Drew Tyre
> Sent: Thursday, April 05, 2012 8:35 AM
> To: Ramiro Barrantes
> Cc: r-help at 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 <
> ramiro at 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 at 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
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> email: atyre2 at unl.edu
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>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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