Problem building R with Intel MKL v10 BLAS

Michael Braun <braunm <at> MIT.EDU> writes:

NO

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.

My config.site file for R is:

#! /bin/sh

R_PAPERSIZE=letter
CFLAGS="-g -O2 -p -pg"
CPPFLAGS="-I/opt/intel/mkl/10.0.1.014/include -I/usr/include 
-I/usr/local/include"
LIBnn=lib64
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 
config.site.file.
I am doing everything as superuser.

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 
suggestions.

Thanks,

Michael

---
I now recall a similar problem with my install of MKL V10. Here is the info:

I got the 10.X, layered library version of MKL 10.X working on R-2.6.1a. I 
set the full path information for the R configuration blas and lapack
option:

--with-blas="-L/.../intel/mkl/10.0.011/lib/em64t -lRblas -lmkl_sequential
-lmkl_lapack -lmkl_core -lpthread"
--with-lapack="-L/.../intel/mkl/10.0.011/lib/em64t -lRlapack -lmkl_sequential
-lmkl_lapack -lmkl_core -lpthread"

In this case, libRblas.so and libRlapack.so are both linked to 
libmkl_gf_lp64.so in the em64t directory. There must be some internal error
in the R configuration and make processing, because it would not pick up the
primary path specification for the mkl libraries location. Instead, I was 
able to define:

*******critical step to get around a possible R bug*******
sh-3.00$ export LD_RUN_PATH=/.../intel/mkl/10.0.011/lib/em64t

After that, I was able to perform the R configure with no errors. Then the
make also worked with no errors. The BLAS_LIBS and LAPACK_LIBS variables
were properly defined, and the path to the MKL libraries was properly
defined in ldpaths:

sh-3.00$ /.../R-2.6.1a/bin/R CMD config BLAS_LIBS
-L/.../intel/mkl/10.0.011/lib/em64t -lRblas -lmkl_sequential -lmkl_lapack
-lmkl_core -lpthread
sh-3.00$ /.../R-2.6.1a/bin/R CMD config LAPACK_LIBS
-L/.../R-2.6.1a/intel/mkl/10.0.011/lib/em64t -lRlapack -lmkl_sequential
-lmkl_lapack -lmkl_core -lpthread
sh-3.00$

power02(43)% more ldpaths
...
${R_LD_LIBRARY_PATH=${R_HOME}/lib:/s/gcc-4.2.1/lib64:
/.../intel/mkl/10.0.011/lib/em64t:/usr/X11R6/lib64:
/.../tcl-8.4.2/i386_rh72/lib:/.../XFree86-4.2.1/i386_rh72/lib}

(... are the various local paths to the objects of interest)

Hope that helps (maybe more than my other post)
MJR