[R] Memory problem with 64bit R using PLASQ500k

From: <Christian.Stratowa_at_vie.boehringer-ingelheim.com>
Date: Mon, 25 Feb 2008 10:42:09 +0100


Dear all,

First I apologize for cross-posting, but I think that this could be of interest to BioC users, too.

For DNA copy-number analysis I have downloaded PLASQ500K from: http://genome.dfci.harvard.edu/~tlaframb/PLASQ/

After creating sub-directories SND and STD containing 3 Sty Mapping arrays each, I tried to compute parent-specific copy number: > library(PLASQ500K)
> psCN <-
pscn(StyFolder="STD",normStyFolder="SND",betasSty=NULL,quantSty=NULL,betasSty File="betasSty.Rdata",rawCNStyfile="rawCNSty.Rdata")

Using only six 250K Sty CEL-files it was impossible to finish this calculation.
On a 32GB RAM Linux server the job got killed, since function EMSNP() which is called from function getBetas() used up all RAM. Starting the computation on our 64GB RAM Linux server, function EMSNP() could be executed, nevertheless, we had to kill the job, when it reached memory consumption of 74GB!!! at a later stage!

Interestingly, when running PLASQ500K on my local workstation, I could finish the computation w/o any memory problems.

So what is the difference:
1. Server (4 Dual-Core AMD Opteron Processors, 64GB RAM): Fedora Core 6 and R-2.6.1 and packages compiled from source for 64-bit. > sessionInfo()
R version 2.6.1 (2007-11-26)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] tcltk tools stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] PLASQ500K_0.0.5 GLAD_1.12.0 aws_1.3-3.1
[4] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1
[7] Biobase_1.16.1

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

2. Workstation (HP xw6400, 2 Intel Xeon Processors, 4GB RAM): Fedora Core 6 and R-2.6.1 and packages compiled from source for 32-bit. > sessionInfo()
R version 2.6.1 (2007-11-26)
i686-pc-linux-gnu

locale:
C

attached base packages:
[1] tcltk tools stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] PLASQ500K_0.0.5 GLAD_1.12.0 aws_1.3-3.1
[4] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1
[7] Biobase_1.16.1

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Does anybody know what might be the reason for this behavior?

Thank you in advance
Best regards
Christian



Christian Stratowa, PhD
Boehringer Ingelheim Austria
Dept NCE Lead Discovery - Bioinformatics Dr. Boehringergasse 5-11
A-1121 Vienna, Austria
Tel.: ++43-1-80105-2470
Fax: ++43-1-80105-2782
email: christian.stratowa_at_vie.boehringer-ingelheim.com

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