R SIG Debian - Jun 2011 - Lapack or Blas crashing R when using "large" matrices (Ubuntu 11.04)

Hello,


This simple SVD calculation (commands are copied immediately below) crashes on
my Ubuntu machine (R 2.13.0). However it
worked fine with R.12 and Ubuntu 10.04, and it also works fine on my Windows 7
machine with R 2.13, so I suspect there's a problem with (my?) Ubuntu and /
or R.

I'm using the R distribution that is accessible with Ubuntu's
repositories manager, I am not building my own.

Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. 

Matias

p <- 500
n <- 300
set.seed(1234)
x <- matrix(rnorm(n*p), n, p)
sih <- var(x)
b <- svd(sih)

produces:
?
?*** caught illegal operation ***
address 0x42b8c9, cause 'illegal operand'

Traceback:
?1: .Call("La_svd", jobu, jobv, x, double(min(n, p)), u, v,?
"dgsedd",???? PACKAGE = "base")
?2: La.svd(x, nu, nv)
?3: svd(sih)
?
I'm using Ubuntu 11.04 and 
>  version
??????????????? _??????????????????????????? 
?platform?????? i686-pc-linux-gnu??????????? 
?arch?????????? i686???????????????????????? 
?os???????????? linux-gnu??????????????????? 
?system???????? i686, linux-gnu????????????? 
?status????????????????????????????????????? 
?major????????? 2??????????????????????????? 
?minor????????? 13.0???????????????????????? 
?year?????????? 2011???????????????????????? 
?month????????? 04?????????????????????????? 
?day??????????? 13?????????????????????????? 
?svn rev??????? 55427??????????????????????? 
?language?????? R??????????????????????????? 
?version.string R version 2.13.0 (2011-04-13)
?
?Thanks,
?
?Matias

Works fine here (Ubuntu 11.04, R 2.13.0 from CRAN):

edd at max:~$ cat /tmp/matias.r 
p <- 500
n <- 300
set.seed(1234)
x <- matrix(rnorm(n*p), n, p)
sih <- var(x)
b <- svd(sih)

cat("All good\n")
edd at max:~$ r /tmp/matias.r 
All good
edd at max:~$ 

Maybe you have the wrong atlas package installed?  What does this yield for
you:

edd at max:~$ dpkg -l | grep "atlas\|blas"
ii  gotoblas2-helper                 0.1-12.local.1                   GotoBLAS2
helper
ii  libatlas-headers                 3.6.0-24ubuntu1                 
Automatically Tuned Linear Algebra Software,C header files
ii  libatlas3gf-base                 3.8.3-29                        
Automatically Tuned Linear Algebra Software, generic shared
ii  libblas-dev                      1.2-8                            Basic
Linear Algebra Subroutines 3, static library
ii  libblas-test                     1.2-8                            Basic
Linear Algebra Subroutines 3, testing programs
ii  libblas3gf                       1.2-8                            Basic
Linear Algebra Reference implementations, shared library
edd at max:~$ 

showing that I use the standard Atlas package from Ubuntu.

Dirk

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