On 21/08/2012 22:46, Marc Schwartz wrote:
On Aug 21, 2012, at 3:39 PM, Bennet Fauber <ben...@umich.edu> wrote:
As a follow-up to my prior post, if I remove --with-blas
--with-lapack, then the stats test passes:
...
Testing examples for package ‘stats’
comparing ‘stats-Ex.Rout’ to ‘stats-Ex.Rout.save’ ... OK
...
Perhaps this is now a question about building R with the Intel MKL
libraries instead of one about the make check.
Thanks, -- bennet
<snip>
Hi,
Three quick comments:
1. I don't have hands on experience with MKL, but would direct you to the R
Installation and Administration Manual section that is relevant:
http://cran.r-project.org/doc/manuals/R-admin.html#MKL
Or even better, the very latest version at
http://r.research.att.com/man/ . As it happens the advice for MKL was
changed last week (MKL itself changes fast).
2. Lower level compiling related queries are best directed to the R-Devel list,
rather than R-Help. If you need to post follow ups, I would suggest that you
subscribe to R-Devel at:
https://stat.ethz.ch/mailman/listinfo/r-devel
and post there.
3. Notwithstanding the above, I presume that you have specific reasons for
using MKL and compiling R from source? Just in case you are not aware, there
are pre-compiled RPM binaries of R 2.15.1 available for RHEL from the EPEL:
http://fedoraproject.org/wiki/EPEL
Installing R from there is as easy as adding the EPEL to your repo list and
using 'yum install R' as root (eg. via sudo) from the CLI.
If you have a modern Intel CPU and need to use large matrices the
speedups can be dramatic. But you trade accuracy for speed: see the
comments in the manual including that --with-lapack is strongly *not
recommended*. Having said that, my MKL build with --with-lapack passes
all its tests on my Xeon E5-5690 (but has not on other CPUs and other
versions of MKL).
More generally, the RPMS are not tuned to your CPU and the right tuning
can speed up R by a few percent.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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