[R-sig-Debian] revolution-mkl package not functioning correctly with R 2.13

Michael Rutter
Thu, 21 Jul 2011 22:59:26 -0000

It appears that the revoluton-mkl package, available via the multiverse
Ubuntu repository with the purpose of adding multi-threaded numeric
libraries to R, is not function correctly with R 2.13 (at least the
version found on CRAN).  Testing with "R-benchmark-25.R" (found at
http://r.research.att.com/benchmarks/), I get the following error, after
installing the revolution-mkl package (4 core, AMD processor, 11.04
64-bit Ubuntu):

 > source("R-benchmark-25.R")
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

     det

Loading required package: SuppDists


    R Benchmark 2.5
    ==============Number of times each test is run__________________________:  3

    I. Matrix calculation
    ---------------------
Creation, transp., deformation of a 2500x2500 matrix (sec):  1.237
2400x2400 normal distributed random matrix ^1000____ (sec):
0.861333333333333
Sorting of 7,000,000 random values__________________ (sec):
1.09133333333333
2800x2800 cross-product matrix (b = a' * a)_________ (sec):
1.55633333333333
Error in solve(crossprod(a), crossprod(a, b)) :
   the leading minor of order 1271 is not positive definite
Timing stopped at: 2.55 0.04 0.729

I was also unable to exit from R cleanly.  I tried R-benchmark-25.R
without the SuppDists package, and the same error occurred.

In a virtual machine, I rolled back R to version 2.12.1, the version
found in the main Ubuntu repository, and R-benchmark-25.R worked without
error.  So it appears that rolling back R to 2.12.1 may be a solution (R
2.12 is no longer available as a deb on CRAN).

I have not tested the GOTOBlas2 libraries.  Ian Fellows mentions issues
on the Mac side of things
(http://groups.google.com/group/deducer/browse_thread/thread/8c9a8af0465f9b9b),
although I am not sure if this applicable as Ubuntu 11.04 is based on
gcc 4.5.

If anyone has the revolution-mkl package working with R 2.13 or has
tested the GOTOBlas2 libraries, please let me know.

Michael

--
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563