[R-sig-Debian] Lapack or Blas crashing R when using "large" matrices (Ubuntu 11.04)

[Matias Salibian-Barrera]

Thanks Dirk. I'm far from a linux power user.

I re-installed the atlas and blas packages, and I removed and re-installed R 2.13 from cran.


Checking for the installed atlas package gives:

matias at tukey:~$ dpkg -l | grep "atlas\|blas"
ii  libatlas-base-dev       3.8.3-29          Automatically Tuned Linear Algebra Software, generic static
ii  libatlas-dev                3.8.3-29         Automatically Tuned Linear Algebra Software, C header files
ii  libatlas-test                3.8.3-29         Automatically Tuned Linear Algebra Software, test programs
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


So it seems everything is fine, but the call to svd() in R still produces:
 *** caught illegal operation ***
address 0x8398c9, 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)

This time, though I also got some more information on the crash:

*** longjmp causes uninitialized stack frame ***: /usr/lib/R/bin/exec/R terminated
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(__fortify_fail+0x50)[0x527df0]
/lib/i386-linux-gnu/libc.so.6(+0xe5d5a)[0x527d5a]
/usr/lib/R/lib/libR.so(+0x1cd6fe)[0x2dd6fe]
[0xfd2400]
/usr/lib/libblas.so.3gf(ATL_join_tree+0x4c)[0x72c34c]

I really don't know what's behind this. Any help / or further pointer would be much appreciated.

Matias






----- Original Message -----
> From: Dirk Eddelbuettel <edd at debian.org>
> To: Matias Salibian-Barrera <msalibian at yahoo.ca>
> Cc: "r-sig-debian at r-project.org" <r-sig-debian at r-project.org>
> Sent: Monday, June 6, 2011 12:55:36 PM
> Subject: Re: [R-sig-Debian] Lapack or Blas crashing R when using "large" matrices (Ubuntu 11.04)
> 
> 
> 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
> 
> -- 
> Gauss once played himself in a zero-sum game and won $50.
>                       -- #11 at http://www.gaussfacts.com
>