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A while back I installed OpenBlas on my Centos server and R 3.02 with great success (over 50% improvement on the R benchmark-25).

I followed the method described in the official R Cran documentation here: http://cran.r-project.org/doc/manuals/r-release/R-admin.html Essentially the suggestion was, rather than re-compile etc. to dynamically linking the new blas creating a symlink using the "old" library name and the new OpenBlas library.

I've now updated my server to 3.1.
I've resolved issues around rstudio installing the preview of the next coming version of rstudio. I created the symlink as per the R manual in the /lib subdirectory, but I've noticed that all the other libraries or symlinks have disappeared. And sadly my symlink seems to be ineffective as the performance have reverted to the original values.

Is there a "simple" way to install openblas (maybe laplak as well?) just through symlinks in R 3.1 & Centos / Fedora?

(I know that similar questions have been asked before, but none seem to specifically address my issue, just emerged with the latest version of Fedora repo)

Enzo
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1 Answers1

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I posted the question on the R-SIG-Fedora mailing list and this morning I've got the following answer from Martyn Plummer (part of R core team and responsible for the R-SIG-Fedora mailing list at R-SIG-Fedora@r-project.org):

This is a change in the way that the RPM is built. The RPM for R 3.1.0
does not build its own blas and lapack libraries, but links directly to
external blas and lapack provided by Fedora.  This means that you can no
longer swap out libRblas.so by replacing it with a symbolic link to
openblas.

If you really want openblas then you should install R from source using
the configure option --with-blas="openblas" (Recall that you need to
install the openblas-devel RPM).

Martyn

I thank Martyn for the prompt reply, and I am sure it has been done for good reasons, but frankly this seems like a functional regression compared to 3.02

Enzo
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  • I think that you might be able to use an 'update-alternatives' solution like that described here for Ubuntu: http://www.stat.cmu.edu/~nmv/2013/07/09/for-faster-r-use-openblas-instead-better-than-atlas-trivial-to-switch-to-on-ubuntu/ – ctbrown Nov 13 '14 at 19:45