Compiling R with MKL

Alex8 — Tue, 28 Jun 2016 17:03:44 GMT

Hi,

I'm trying to compile R 3.3.1 on Ubuntu Server 16.04 with Intel MKL using the GNU Fortran and C compilers. Unfortunately, I'm unable to get the gcc to locate BLAS. I've tried several combinations of suggestions between those on the Intel website, including Build R-3.0.1 with Intel MKL, Using Intel MKL with R, and the Intel Link Advisor. I've also found some other bloggers who have successfully compiled R with MKL. Unfortunately, no one else's solutions have worked for me thus far.

I first ran the provided shell script to set the environment variables. I've noticed it's the INCLUDE variable is empty. Is this a problem, or did it happen by design? All others are appropriately created.

I've also been specifying the following LDFLAGS="-L$MKLROOT/lib/intel64" or LDFLAGS = "-L$MKLROOT/include" in order to point gcc to the directories. When I check config.log after the configuration, however, I see:

configure: 31659: checking for dgemm_ in -lblas
configure: 31692: gcc -o conftest -march=native -O3 -I/usr/local/include -L/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/include conftest.c -lblas -lgfortran -lm -lquadmath -lrt -ldl -l > &5
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status

for both settings of the LDFLAGS.

Any suggestions would be tremendously appreciated! Thank you for your time!

Hi again,

Alex8 — Tue, 28 Jun 2016 17:59:56 GMT

Hi again,

I was able to solve this problem with the following settings:

MKLROOT is set by the Intel-provided shell script
LDFLAGS="-L$MKLROOT/lib/intel64 -m64"
MKL="-L$MKLROOT/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -fopenmp -lpthread -lm -ldl"
./configure --with-blas="$MKL" --with-lapack

Alex

Hi Alex,

Ying_H_Intel — Wed, 29 Jun 2016 01:04:50 GMT

Hi Alex,

Glad to know you are able to solve the problem and thank you a lot for the sharing.

Best Regards,

Ying

topic Hi again, in Intel® oneAPI Math Kernel Library

Compiling R with MKL

Hi again,

Hi Alex,