[R-sig-Debian] Accessto OpenBLAS

[Scott Raynaud]

So my experiments have confirmed that the binary version of
OpenBLAS uses onlt two cores.  Should the compiled version
use more?

I want figure out which package to utilize mulitiple cores in
a UNIX environment.  Did some research on this a while back 
but it's a bit fuzzy right now.  My main concern is there's a 
warning about BLAS and multiple cores in the install docs.
Will I run into problems?

 
----- Original Message -----
From: Michael Rutter <mar36 at psu.edu>
To: Dirk Eddelbuettel <edd at debian.org>
Cc: Scott Raynaud <scott.raynaud at yahoo.com>; "r-sig-debian at r-project.org" <r-sig-debian at r-project.org>
Sent: Tuesday, February 14, 2012 6:47 PM
Subject: Re: [R-sig-Debian] Accessto OpenBLAS



On 02/14/2012 06:40 PM, Dirk Eddelbuettel wrote:
>
> 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.

That package is hard to find without Dirk's gcdb vignette.  Here is the 
link:

http://prs.ism.ac.jp/~nakama/debian/lenny-ism/

That would work to install GotoBLAS. Reworking the helper package for 
OpenBLAS would make a nice little project.  There is an OpenBLAS package 
for Ubuntu 11.10, but the binary version only uses two cores, at least 
that what it used the last time I tried it.


> 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
>      recall).

My guess is that the manual steps are the ones I described above.

Michael

> 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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>

-- 
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