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 > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
