R on Mac building up memory usage
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 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en http://depsy.org/person/434412