[R-sig-Geo] R crashed when running calc

[Jonathan Greenberg]

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)
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>         [[alternative HTML version deleted]]
>
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-- 
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/
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