[BioC] Memory and vector size management on linux 64bit

[Benilton Carvalho]

what do you get when you run:

.Machine[["sizeof.pointer"]]

?

I'm really surprised by the "i486-pc-linux-gnu" bit from your
sessionInfo()... I'd expect something like x86_64, if you were running
a 64 bit version of R.

Given that you're running Ubuntu, you're expected to follow the steps
as described by the page below:

http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/

b

On Fri, Apr 16, 2010 at 5:30 PM, Manca Marco (PATH)
<m.manca at path.unimaas.nl> wrote:
>
> Dear fellow bioconductors,
>
> good afternoon.
>
> I am encountering an error concerning the allocations of vectors bigger than a certain size. My problem is that said size is far below the amount of RAM I have installed on the system.
>
> Following some previous threads on the topic I have at first thought that my RAM could have been temporarily unavailable thus I have monitored the memory usage and the error message appeared when just 2,5Gb were in use out of the about 7 Gb available.
>
> The system is running linux Ubuntu Hardy Heron 64bit, and it sports a Xeon CPU and 8Gb of RAM.
>
> Following I am pasting my code and my sessionInfo()
>
> # Charging my microArray data (44 human whole genome by Illumina)
>>library(lumi)
>>fileName <- "MyExperiment_no_32_no_tech_duplos.csv";
>>library(lumiHumanAll.db)
>>Data.Immature <- lumiR(fileName, lib="lumiHumanAll.db");
>>Data <- lumiExpresso(Data.Immature, QC.evaluation=TRUE);
>
> # Extract expression data from lumi object:
>>Expression <- exprs(Data)
>>names(Expression) <- Data at phenoData@data$sampleID
>
> # Calculate distance matrix for cluster analysis
>>distance=dist(Expression, method="euclidean")
> Error: cannot allocate vector of size 1.8 Gb
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> i486-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] lumiHumanAll.db_1.8.1 org.Hs.eg.db_2.3.6    lumi_1.12.4
>  [4] MASS_7.3-5            RSQLite_0.8-3         DBI_0.2-5
>  [7] preprocessCore_1.8.0  mgcv_1.6-1            affy_1.24.2
> [10] annotate_1.24.1       AnnotationDbi_1.8.1   Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0      grid_2.10.1        lattice_0.18-3     Matrix_0.999375-37
> [5] nlme_3.1-96        tools_2.10.1       xtable_1.5-6
>
>
>
> Reading this page ( http://stat.ethz.ch/R-manual/R-patched/library/base/html/Memory.html ) I have come to hypothesize that there could be some vector size limit indipendent from the RAM availability, but I wonder whether it is true on a 64bit machine and how  could I circumvent  the problem:
>
> 1) any suggestion on how to modify the vector size threshold (if it exists)?
>
> 2) any suggestion on how to force the dist function to strip  down the matrix into smaller vectors?
>
>
> Thank you in advance for your attention and for any feedback.
>
> All the best, Marco
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debeijelaan 25, 6229  HX Maastricht
>
> E-mail: m.manca at path.unimaas.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
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