[Rd] Problem building R with Intel MKL v10 BLAS
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Jan 25 07:35:41 CET 2008
On Thu, 24 Jan 2008, Michael Braun wrote:
> Hi. I'm not sure if this is an R-help or R-devel problem, so I'm
> starting here in the hope that someone can help (and willing to go to
> the other list if it's more appropriate). I think I am following all of
> the instructions in the various manuals, but clearly I am missing something.
> I have an Intel EM64T Dell with 2 dual-core Xeon processors running Red
> Hat EL5. I would like to build R 2.6.1 with lots of debugging and
> profiling options, and link it to the processor-specific Intel MKL blas.
> The problem is that after I compile R, and do R CMD config BLAS_LIBS,
> the response is
> -L/usr/local/lib64/R/lib -lRblas.
> This tells me that R is not linked to the Intel BLAS at all.
Not so, because Rblas contains any links to an external BLAS. Check over
the R-admin manual and note that --enable-BLAS-shlib is the default.
So you need to check
to see if it linked to MKL.
Check over config.log to see what happened: a common problem is that the
libraries are not known to ld.so (you may need to include
/opt/intel/mkl/10.0.1.014/lib/em64t in LD_LIBRARY_PATH)
> My config.site file for R is:
> #! /bin/sh
> CFLAGS="-g -O2 -p -pg"
> CPPFLAGS="-I/opt/intel/mkl/10.0.1.014/include -I/usr/include
> BLAS_LIBS="-L/opt/intel/mkl/10.0.1.014/lib/em64t -Wl,--start-group
> -lmkl_gf_lp64.so -lmkl_gnu_thread.so -lmkl_core.so -l -l -l -Wl,
> --end-group -lguide -lpthread -lm"
> I have set the CONFIG_SITE environment variable to the location of the
> I am doing everything as superuser.
What compilers are you using? That would appear to be using
gcc/gfortran and not the Intel compilers.
> The command I am using for configure is
> ./configure --disable-R-profiling --with-blas=no
> following the instructions in the R-admin file regarding enabling
> C-level profiling and linking to the external BLAS libraries referenced
> in the config.site file.
> The BLAS_LIBS files are different than in the R-admin manual because of
> changes in the Intel MKL for version 10. These libraries, in this
> order, were taken from the Intel MKL for Linux User's Guide, chapter 5.
> So, still no luck linking to the optimized BLAS. I'd appreciate any
Brian D. Ripley, ripley at 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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