[R] Fwd: compiling R with tuned BLAS

Michael J Gooch goochmi at gmail.com
Sat May 23 19:58:25 CEST 2015

forgot to include the list on cc

-------- Forwarded Message --------
Subject: 	Re: [R] compiling R with tuned BLAS
Date: 	Fri, 22 May 2015 10:40:13 -0400
From: 	Michael Gooch <goochmi at gmail.com>
To: 	Charles Determan <cdetermanjr at gmail.com>

I am not an administrative user. I'm using a university cluster and have 
to build everything and its dependencies manually.

I cannot use update alternatives, as it is a centos machine and as 
mentioned, I am not a sudoer. I have been setting up the various tools 
with http://modules.sourceforge.net/.

M. Gooch

On 05/22/2015 08:16 AM, Charles Determan wrote:
> Which OS are you using (Windows, Linux (distro), Mac)? When you 
> mention .so files I tend to assume you are using a Linux system.  If 
> you are using ubuntu, changing the BLAS used by R is relatively 
> trivial by using 'update-alternatives'.  More detail is provided at 
> the following link: 
> http://www.stat.cmu.edu/~nmv/2013/07/09/for-faster-r-use-openblas-instead-better-than-atlas-trivial-to-switch-to-on-ubuntu/ 
> <http://www.stat.cmu.edu/%7Enmv/2013/07/09/for-faster-r-use-openblas-instead-better-than-atlas-trivial-to-switch-to-on-ubuntu/>
> Charles
> On Thu, May 21, 2015 at 2:19 PM, Michael Gooch <goochmi at gmail.com 
> <mailto:goochmi at gmail.com>> wrote:
>     I am looking at the instructions on
>     http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#ATLAS
>     I have noticed that ATLAS produces two shared libs in addition to
>     the *.a files:
>     http://math-atlas.sourceforge.net/atlas_install/node22.html
>     contents of the ATLAS lib directory:
>     libatlas.a  libcblas.a  libf77blas.a  liblapack.a libptcblas.a
>     libptf77blas.a  libsatlas.so  libtatlas.so
>     The instructions do not appear to match up with the *.a files &
>     *.so files as described. (it appears to want me to use shared
>     libs, but the names defined are static libs, not shared libs).
>     should I simply be having it link against libtatlas.so (and
>     pthreads) for shared threaded atlas and libsatlas.so for shared
>     sequential atlas?
>     do I need shared versions of the other static libraries?
>     I think the help is a bit out of date, or at least unclear as to
>     what it intends of me.
>     M. Gooch
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