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R crashed when running calc
6 messages · Eddie Smith, Robert J. Hijmans, Jonathan Greenberg
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Eddie, The function does not work (maxsst is not defined). You are not providing sessionInfo() You should be able to avoid memory problems (if that is what causes this) via rasterOptions(chunksize=___) E.g., rasterOptions(chunksize=1e+05) Robert
On Mon, Feb 17, 2014 at 11:19 AM, Eddie Smith <eddieatr at gmail.com> wrote:
Hi guys,
Everytime I tried to run calc(), R crashed. Any advice?
Here is my code:
#clear memory/remove all R objects
rm(list=ls())
#check memory size and set memory limit
memory.size()
memory.limit(10000)
#Load related packages library
library(raster)
library(rgdal)
#Load all raster data in a folder
img <- list.files(pattern='\\.img$')
#Check rasters
list(img)
#Stack layers into one file
flag7 <- stack(img)
#2 CReate fun
time <- 1:nlayers(flag7)
fun <- function(x) {
if (all(is.na(x))) {
return(cbind(NA,NA,NA))
}
xcost<-cos(2*pi*time/366)
xsine<-sin(2*pi*time/366)
m = lm(x~xcost+xsine)
s <- summary(m)
maxval <- max(predict(m))
r2 <- s$r.squared
sigma <- s$sigma
cbind(maxsst, r2, sigma)
}
#3 Run function with rasterstack
r <- calc(flag7, fun)
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Eddie: This is the Windows x64 version of R 3.0.2, right? I found that the x64 release for whatever reason R needs to be launched with the --max-mem-size=XXXM flag if you want more than 2gb available to R. XXX is the number of megabytes to give it access to. This seemed to have been a change from 3.0.1 (which seemed to set the memory to be the max available on the system). Give this a shot when you launch it. Check http://stackoverflow.com/questions/1395229/increasing-the-memory-available-to-r-processes for some hints on this (you can append the setting to your GUI shortcut). You should also follow Robert's suggestion and set the chunkSize to be VERY small if the max-mem-size doesn't work. --j
On Tue, Feb 18, 2014 at 7:08 AM, Eddie Smith <eddieatr at gmail.com> wrote:
Thank you very much Robert. Tried to increase to set the chunksize as suggested( rasterOptions(chunksize=1e+05)) but still no luck. The full session is:
sessionInfo()
R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rgdal_0.8-16 raster_2.2-12 sp_1.0-14 loaded via a namespace (and not attached): [1] grid_3.0.2 lattice_0.20-24 My rasterstack is huge but I haven't got any problem with this rasterstack before.
flag7
class : RasterStack dimensions : 1032, 1656, 1708992, 10592 (nrow, ncol, ncell, nlayers) Thanks. On Tue, Feb 18, 2014 at 2:59 AM, Robert J. Hijmans <r.hijmans at gmail.com>wrote:
Eddie, The function does not work (maxsst is not defined). You are not providing sessionInfo() You should be able to avoid memory problems (if that is what causes this) via rasterOptions(chunksize=___) E.g., rasterOptions(chunksize=1e+05) Robert On Mon, Feb 17, 2014 at 11:19 AM, Eddie Smith <eddieatr at gmail.com> wrote:
Hi guys,
Everytime I tried to run calc(), R crashed. Any advice?
Here is my code:
#clear memory/remove all R objects
rm(list=ls())
#check memory size and set memory limit
memory.size()
memory.limit(10000)
#Load related packages library
library(raster)
library(rgdal)
#Load all raster data in a folder
img <- list.files(pattern='\\.img$')
#Check rasters
list(img)
#Stack layers into one file
flag7 <- stack(img)
#2 CReate fun
time <- 1:nlayers(flag7)
fun <- function(x) {
if (all(is.na(x))) {
return(cbind(NA,NA,NA))
}
xcost<-cos(2*pi*time/366)
xsine<-sin(2*pi*time/366)
m = lm(x~xcost+xsine)
s <- summary(m)
maxval <- max(predict(m))
r2 <- s$r.squared
sigma <- s$sigma
cbind(maxsst, r2, sigma)
}
#3 Run function with rasterstack
r <- calc(flag7, fun)
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_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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