I think any geostatistical program/R package would have trouble handling 12000 observations on a PC. The empirical variogram would be built with the combinations of 12000 over 2 pairs, nearly 72 millions pairs, and during kriging, if you didn't restrict the search neighbourhood, interpolation would involve solving something very big, more so if you defined a fine grid, ... Try restricting the search neighbourhood, if you didn't, with maxdist and nmax.
Rubén Prof Brian Ripley wrote: > I think the clue is that the message you quote comes from gstat, which > does not use R's memory allocator. It is gstat and not R that has failed > to allocate memory. > > Try re-reading the help page for memory.size. 'max=T' does not indicate > the limit (that is the job of memory.limit()), but the maximum 'used' > (acquired from the OS) in that session. So 19Mb looks reasonable for R's > usage. > > I don't understand the message from memory.limit() (and the formatting is > odd). memory.limit() does not call max() (it is entirely internal), so I > wonder if that really is the output from that command. (If you can > reproduce it, please let us have precise reproduction instructions.) > > There isn't much point in increasing the memory limit from the default > 1.5Gb on a 2Gb XP machine. The problem is that the user address space > limit is 2Gb and fragmentation means that you are unlikely to be able to > get over 1.5Gb unless you have very many small objects, in which case R > will run very slowly. In any case, that is not the issue here. > > On Wed, 16 Apr 2008, Dave Depew wrote: > >> Hi all, >> I've read the R for windows FAQ and am a little confused re: >> memory.limit and memory.size >> >> to start using R 2.6.2 on WinXP, 2GB RAM, I have the command line "sdi >> --max-mem-size=2047M" >> Once the Rgui is open, memory.limit() returns 2047, memory.size() >> returns 11.315, and memory.size(max=T) returns 19.615 >> >> Shouldn't memory.size(max=T) return 2047? >> >> Upon running several operations involving kriging (gstat package, >> original data file 3 variables, 12000 observations) >> the program runs out of memory >> >> "memory.c", line 57: can't allocate memory in function m_get() >> Error in predict.gstat(fit.uk, newdata = EcoSAV.grid.clip.spxdf, >> debug.level = -2, : >> m_get >> >> Immediately following this, >> >> memory.limit() returns [1] -Inf >> Warning message: >> In memory.limit() : no non-missing arguments >> to max; returning -Inf >> >> memory.size() returns 24.573. >> >> memory.size(max=T) returns 46.75 >> >> To my untrained eye, it appears that R is not being allowed access to >> the full memory limit specified in the cmd line....if this is the case, >> how does one ensure that R is getting access to the full allotment of RAM? >> Any insight is appreciated... >> >> >>> sessionInfo() >> R version 2.6.2 (2008-02-08) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets tcltk utils >> methods base >> >> other attached packages: >> [1] maptools_0.7-7 foreign_0.8-23 gstat_0.9-43 rgdal_0.5-24 >> lattice_0.17-4 sp_0.9-23 svSocket_0.9-5 svIO_0.9-5 >> R2HTML_1.58 svMisc_0.9-5 svIDE_0.9-5 >> >> loaded via a namespace (and not attached): >> [1] grid_2.6.2 tools_2.6.2 >> >> ______________________________________________ >> 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. >> > ______________________________________________ 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.
