[R] R with MKL

Martyn Plummer plummer at iarc.fr
Tue Mar 17 10:37:06 CET 2009

On Mon, 2009-03-16 at 18:33 -0400, Cristián wrote:
> Hi,
> I have seen a lot of problems from people trying to compile R with
> MKL. So I am writing my experience in case it helps and to ask one
> question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using

The R-admin manual has been updated with instructions for MKL since the
last thread on the topic. You should look there in section A.3.1.4.
> I configured correctly (following MKL userguide) with :
> sudo ./configure --with-blas="-I/opt/intel/mkl/
> -L/opt/intel/mkl/ -lmkl_intel_lp64
> -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
> --with-lapack="-I/opt/intel/mkl/
> -L/opt/intel/mkl/ -lmkl_intel_lp64
> -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
> But in order to compile had to edit src/modules/lapack/vecLibg95c.c
> and comment out the include. Weird, since I am not building for Mac.

OK. There are two things happening here. 

You are using the wrong interface layer. With gcc you need to use
-lmkl_gf_lp64, since the way that complex numbers are represented
differs between Intel and GNU compilers.

There is a known workaround for this problem for MacOs X, using the
cblas interface.  Apparently, this workaround is also being applied
here.  I will look into it.

> Make check returned no error. I checked with ldd that R is linked
> against MKL. All demos run
> I set MKL_NUM_THREADS={1,2} environment var and run R-benchmark-25.R
> from (http://r.research.att.com/benchmarks/R-benchmark-25.R). Not all
> tests use MKL so you get around 20% improvement for 2 cores. Also
> monitoring with top you can see which tests use 2 cores.
> Question: Am I set? What was that error relating to vecLib? I need to
> install now on a bigger multicore server for data-mining and dont want
> to deliver a defective installation. Maybe I could run a larger
> check-benchmark.
> Thanx a lot,
> C.
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