On 02.10.2010 03:10, Peter Langfelder wrote:
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).
But not too funny given you have only 8Gb in your machine.
So the answer probably is: Buy more RAM or try to reduce the problem.
Peter
On Fri, Oct 1, 2010 at 6:02 PM, Mete Civelek<mcive...@mednet.ucla.edu> wrote:
Hi Everyone,
I am getting the following error message
Error: cannot allocate vector of size 2.6 Gb
So just the next step is about allocating 2.6 Gb! Note that you had only
2.6Gb free at all given the information you specified below. Hence it
won't work on any OS, if you limit R to 8Gb.
Uwe Ligges
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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