[R] Memory problem ... Again

[Liaw, Andy]

Have you checked whether there are limits set?  What does `ulimit -a' say?
Do you know how much memory the R process is using when the error occurred?
We've had R jobs using upwards of 13GB on a box with 16GB of RAM (SLES8 on
dual Opterons) and never had problems.

Andy



> From: Tae-Hoon Chung
> 
> Happy new year to all;
> 
> A few days ago, I posted similar problem. At that time, I 
> found out that our
> R program had been 32-bit compiled, not 64-bit compiled. So 
> the R program
> has been re-installed in 64-bit and run the same job, reading in 150
> Affymetrix U133A v2 CEL files and perform dChip processing. 
> However, the
> memory problem happened again. Since the amount of physical 
> memory is 64GB,
> I think it should not be a problem. Is there anyway we can 
> configure memory
> usage so that all physical memory can be utilized?
> 
> Our system is like this:
> System type: IBM AIX Symmetric Multiprocessing (SMP)
> OS version: SuSe 8 SP3a
> CPU: 8
> Memory: 64GB
> 
> The codes are as follows:
> > Data <- ReadAffy(filenames = paste(HOME, "CelData/", fname, sep=""))
> > eset <- expresso(Data, normalize.method="invariantset", 
> bg.correct=FALSE, pmc\
> orrect.method="pmonly", summary.method="liwong")
> normalization: invariantset
> PM/MM correction : pmonly
> expression values: liwong
> normalizing...Error: cannot allocate vector of size 594075 Kb
> > gc()
>            used  (Mb) gc trigger   (Mb)
> Ncells   797971  21.4    1710298   45.7
> Vcells 76716794 585.4  305954055 2334.3
> ...
> > mem.limits()
> nsize vsize
>    NA    NA
> > object.size(Data)
> [1] 608355664
> > memory.profile()
>     NILSXP     SYMSXP    LISTSXP     CLOSXP     ENVSXP    
> PROMSXP    LANGSXP
>          1      30484     372383       4845        420        
> 180     127274
> SPECIALSXP BUILTINSXP    CHARSXP     LGLSXP                   
>         INTSXP
>        203       1168     111430       5296          0        
>   0      44650
>    REALSXP    CPLXSXP     STRSXP     DOTSXP     ANYSXP     
> VECSXP    EXPRSXP
>      13382          9      60170          0          0      
> 26003          0
>   BCODESXP  EXTPTRSXP WEAKREFSXP
>          0        106          0
> 
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