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

[ivo welch]

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
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
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)