[R] Memory allocation in 64 bit R

[Peter Langfelder]

Hi Mete,

I think you should look at the help for memory.limit. Try to set a
higher one, for example

memory.limit(16000)

(I think 16GB is what xenon will take).

Peter

On Fri, Oct 1, 2010 at 6:02 PM, Mete Civelek <mcivelek at mednet.ucla.edu> wrote:
> Hi Everyone,
>
> I am getting the following error message
>
> Error: cannot allocate vector of size 2.6 Gb
> In addition: Warning messages:
> 1: In dim(res$res) = dim(bi) :
>  Reached total allocation of 8122Mb: see help(memory.size)
> 2: In dim(res$res) = dim(bi) :
>  Reached total allocation of 8122Mb: see help(memory.size)
> 3: In dim(res$res) = dim(bi) :
>  Reached total allocation of 8122Mb: see help(memory.size)
> 4: In dim(res$res) = dim(bi) :
>  Reached total allocation of 8122Mb: see help(memory.size)
>
> Here is the relevant info
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   tcltk     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] cluster_1.12.3      WGCNA_0.93          Hmisc_3.8-2
> [4] survival_2.35-8     qvalue_1.22.0       flashClust_1.00-2
> [7] dynamicTreeCut_1.21 impute_1.22.0
>
> loaded via a namespace (and not attached):
> [1] grid_2.11.1     lattice_0.19-11 tools_2.11.1
>
>> memory.size(NA)
> [1] 8122.89
>> memory.size()
> [1] 5443.18
>> memory.limit()
> [1] 8122
>> .Machine$sizeof.pointer
> [1] 8
>
> And this is what I am trying to do when I get this error message
>> ls()
> [1] "datExpr"
>> print(object.size(datExpr), units = "auto")
> 23.5 Mb
>> ADJ1=((1+bicor(datExpr, use="pairwise.complete.obs", maxPOutliers=0.05, quick=0, pearsonFallback="individual"))/2)^8
>
> If I understand the archives correctly my problem is with memory allocation of a large vector to the address space. Is there any way to get around this without having to use a Linux system?  Has anyone been able to solve this problem?
>
> I appreciate any suggestions or help.
>
> Mete Civelek
>
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