[R-sig-Debian] stock ubuntu raring binary R 3.0.1 and accelerated blas libraries?

[Dirk Eddelbuettel]

On 23 June 2013 at 18:47, ivo welch wrote:
| thank you, dirk.  this was a very good explanation--and thank you for
| having made the binaries available to us.  mint is based on ubuntu and
| shares its repositories.  it's really the same basic OS, just an
| old-stylish desktop GUI.  to summarize the most critical part of your

Whtever floats your boat.  You can install several different desktop
frameworks at once on stock Ubuntu or Debian -- even my old and tiny netbook
has Ubuntu Unity, Kubuntu (KDE), stock Ubuntu Gnome, Lubuntu (LXDE), Xubuntu
(XFCE) and Cinnamon just for comparison.  Not unlike BLAS libraries ....

| response for the google search, the way to check whether atlas is
| installed (short of just benchmarking it and seeing the speed up) were
| your lines
| 
| $ ls -l /usr/lib/libblas.so.3 /etc/alternatives/libblas.so.3
| lrwxrwxrwx 1 root 38 Jun 23 18:08 /etc/alternatives/libblas.so.3 ->
| /usr/lib/atlas-base/atlas/libblas.so.3
| lrwxrwxrwx 1 root 30 May 24 10:23 /usr/lib/libblas.so.3 ->
| /etc/alternatives/libblas.so.3
| 
| and the first line indeed shows that I am now using libatlas.  grin.
| elegant mechanism, actually, but a little obscure when one does not
| know it.
| 
| the speedup for me is spectacular.  on simon urbanek's R-benchmark-25,
| my time goes from 30.3 sec to 9.6 sec on an i7-2660k.  and watching my
| CPU usage with top, this seems to be the single-threaded version of
| atlas, too.
| 
| is it possible and/or would it make sense to add libatlas as a
| dependency for r-base in the ubuntu .deb package, so that it is
| automatically installed, too?  novices won't realize how they can

Did you even look at, say, 'apt-cache show r-base-core | grep Depends:' ?

I seem to have anticipated this very good suggestion a good nine years ago in
2004, see /usr/share/doc/r-base-core/changelog.Debian.gz :

[...]

  
  * debian/control: Changed Build-Depends from 'blas-dev (>=1.0-9),lapack-dev'
     to 'refblas3-dev | atlas3-base-dev, lapack3-dev | atlas3-base-dev'
  * debian/control: Dito for Depends: for r-base-dev 
  * debian/rules: Set configure arguments for refblas3/atlas3 and 
    lapack3/atlas3, respectively, instead of blas/atlas v2.

 -- Dirk Eddelbuettel <edd at debian.org>  Sun, 29 Feb 2004 16:55:55 -0600

[...]

There are few more entries related to atlas there.

Dirk


| speed up R so easily, and experts can easily override it with their
| own choice library.  libatlas can be assumed to be in the ubuntu
| repository.  would there be a serious drawback that I am not
| realizing?  this is of course for the general public's sake--I now
| know how to do this and check this.
| 
| regards,
| 
| /iaw
| 
| ----
| Ivo Welch (ivo.welch at gmail.com)

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com




-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com