[R-sig-Debian] Accessto OpenBLAS

Dirk Eddelbuettel edd at debian.org
Wed Feb 15 00:40:30 CET 2012

On 14 February 2012 at 18:15, Michael Rutter wrote:
| On 02/14/2012 04:56 PM, Scott Raynaud wrote:
| > My IT people have set up R on a a Kubuntu box with an RWkard
| > front end.  I have OpenBLAS set up as a shared BLAS but I'm not
| > sure how to get R to see it.  A.3.1 of the installation docs talks
| > about it but I'm not clear if I need a option on my startup line or
| > if I need to find a config file.  The BLAS is is in:
| >
| > /usr/lib/openblas-base
| >
| > on my machine. I'm not sure how to confirm that R is seeing
| > the BLAS.
| >
| > Recommendations?
| >
| Scott,
| There used to be a good post about this on a blog, but the blog has gone 
| under.  Luckily, I was able to salvage the post from Google cache.  Here 
| is the relevant part:
|      Copy the resulting .so shared object library file 
| (libgoto2_penrynp-r1.12.so on my machine) to /usr/lib
|      The original BLAS library located there is called libblas.so.3gf.0. 
|   Back this file up:  cp libblas.so.3gf.0  libblas.so.3gf.0.keep
|      Make a symbolic link to the new BLAS library:
|      ln -s libgoto2_penrynp-r1.12.so libblas.so.3gf.0
| Basically, you need to make sure that the file "libblas.so.3gf.0" links 
| to the location of your lib.  I would find a benchmark file 
| (http://r.research.att.com/benchmarks/) to test R before and after 
| creating the link, just to make sure it is working.

Is that really needed?

a)  We never had Goto in the distro for its licensing issues. But there
    always was the goto2helper package from Japan which I and other have
    used with great success.

    With it, goto BLAS became a drop-in just like Atlas or MKL.

b)  I haven't had time play with Openblas but I recall Doug Bates telling me
    it worked for him (possibly after one or two manual steps I cannot

c)  I hope to get to OpenBlas myself 'soon' and may follow-up then.

Lastly, and as always, faster BLAS are nice, but BLAS are rarely your
bottleneck with R.

Hope this helps, Dirk

| Hope this helps,
| Michael
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| -- 
| Dr. Michael A. Rutter
| School of Science
| Penn State Erie, The Behrend College
| Station Road
| Erie, PA 16563
| http://math.bd.psu.edu/faculty/rutter
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