[R-sig-Geo] R on Mac building up memory usage

[Roger Bivand]

On Fri, 27 May 2016, Dr Didier G. Leibovici wrote:

> Hi,
>
> I guess this may be not a specificity of r-sig-geo but as I am using
> library(rgdal)
> library(rgeos)
>
> in this script so it may be the reason? (perhaps I should try running
> something else to check).
>

Hi Didier,

Trying a bare bones script may be sensible. There shouldn't be anything in 
those packages that creates these effects as such. How many cores are 
running R simultaneously? There shouldn't be anything OSX-specific either, 
though memory management varies across platforms (there was a recent 
discussion on R-devel about this).

So if you could share such a bare-bones script and simulated data setup, 
others might be able to contribute.

Best wishes,

Roger

>
> So basically I am running some code reading  61288 features and other
> things ... if I run it once I got in gc():
> > gc()
>           used (Mb) gc trigger  (Mb) max used  (Mb)
> Ncells 1833926 98.0    5103933 272.6  9968622 532.4
> Vcells 2437534 18.6    7056348  53.9 11036325  84.3
>
> and on the monitor it says R is using 3.3Go.
>
> Then I remove everything rm(list=ls()) and run it again trying different
> sets of parameters for example.
> Second run similar gc() but R is using 6.4Go
> > gc()
>           used (Mb) gc trigger  (Mb) max used  (Mb)
> Ncells 1834325 98.0    6323353 337.8  9968622 532.4
> Vcells 2439267 18.7    7572947  57.8 11832730  90.3
>
>
> After a while and few other computation I get R is using 10Go
> and gc() gives
> > gc()
>           used (Mb) gc trigger  (Mb)  max used  (Mb)
> Ncells 1863272 99.6    5944937 317.5   9968622 532.4
> Vcells 2503503 19.2    8462995  64.6 100858653 769.5
> rm(list=ls())
> > ls()
> character(0)
> >gc()
>          used (Mb) gc trigger  (Mb)  max used  (Mb)
> Ncells 608451 32.5    4755949 254.0   9968622 532.4
> Vcells 760517  5.9    6770396  51.7 100858653 769.5
>
> but  still 10Go for R in the monitor.
> I had experienced a building up to 50Go then my system tells me to close
> some apps, all that doing the same running one set, then rm(list=ls())
> ... So at the moment I just have to close and re-start R?
>
> Didier
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
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