R devel - May 2008 - problem building R packages on RHEL 4 Linux with Intel compilers

I would like to build R and packages with the Intel 10.1 compilers in RHEL4.
Using the flags below, I can successfully build R using a vanilla
./configure, but when I install new packages they build with gcc. My
sysadmin suggested adding the flags to ./configure as illustrated below, but
then the R build blows up with the config tail output that follows far
below. It looks like gcc is still being searched for. I did read the R
install and admin manual but could not find an answer. Help?

CC=icc
CFLAGS="-fast -unroll"
F77=ifort
FLAGS="-fast -unroll"
CXX=icpc
CXXFLAGS="-fast -unroll"
FC=ifort
FCFLAGS="-fast -unroll"
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64"
SHLIB_CXXLD=icpc
../configure --prefix=/N/u/mkimpel/Quarry/R_HOME/R-patched/R-build\
CC=icc CFLAGS="-fast -unroll -wd188" F77=ifort FFLAGS="-fast
-unroll" \
CXX=icpc CXXFLAGS="-fast -unroll" FC=ifort FCFLAGS="-fast
-unroll" \
ICC_LIBS=/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/lib \
IFC_LIBS=/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/lib \
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64" \
SHLIB_CXXLD=icpc; gmake; gmake install
###########################

checking for gcc... gcc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.


-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

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Mark Kimpel wrote:
> 
> checking for gcc... gcc
> checking for C compiler default output file name...
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
Are you running this as root? Or do you have the right
privileges for the install?

The "cannot create executables" looks like a permission problem

Esmail

"Mark Kimpel" <mwkimpel at gmail.com> writes:
> I would like to build R and packages with the Intel 10.1 compilers in
RHEL4.
We are successfully building R and packages with the Intel 10.1
compilers on RHEL4 (except a few packages, which will not compile with
10.1, but with 9.1).  We also use the Intel MKL blas/lapack libraries.

This is out procedure for building R:

export CC="icc"
export CFLAGS="-O3 -ip -wd188"
export F77="ifort"
export FFLAGS="-O3 -ip"
export CXX="icpc"
export CXXFLAGS="-O3 -ip"
export FC="ifort"
export FCFLAGS="-O3 -ip -mp"

./configure --prefix="/site/VERSIONS/R-2.7.0" \
  --with-blas="-L/site/intel/cmkl/8.1/lib/em64t -lmkl -lvml -lguide
-lpthread" \
  --with-lapack="-L/site/intel/cmkl/8.1/lib/em64t -lmkl_lapack64
-lmkl" \
  --enable-R-shlib

make -j 4

make -j 4 check # NB! "-j 4" won't work on all versions of R

make install

Packages are installed with install.packages() in R.  The procedure is
loosely based on the Intel/MKL examples given in the R Installation and
Administration Manual.

The only thing we haven't figured out how to solve, is how to also
generate the libRblas.so and libRlapack.so; --enable-BLAS-shlib seems to
interfer with the --with-lapack, such that the extarnal library will not
be used.

-- 
Regards,
Bj?rn-Helge Mevik