topic Building R with MKL in Intel® oneAPI Math Kernel Library

Building R with MKL

syk — Wed, 10 Mar 2021 13:03:01 GMT

Hello,

I am new to intel c++ compiler.

Further to installation of 2017 intel c++ composer edition, I am trying to build R with Intel MKL, following this link

https://software.intel.com/content/www/us/en/develop/articles/using-intel-mkl-with-r.html

In particular,

"building R with GNU gcc and GNU gfortran, to use the GNU OpenMP* threaded version of Intel® MKL in R on a Linux operating system"

=====

$ MKL="-Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm"

...

checking for dgemm_ in -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm... no
configure: error: BLAS was specified but not available

=======

When I check R config.log, I find

=====

configure:41233: checking for dgemm_ in -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm
configure:41255: /usr/local/bin/gcc-10 -o conftest -g -O2 -fpic -I/usr/local/include -L/usr/local/lib64 conftest.c -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -lgfortran -lm -lquadmath -lrt -ldl -lm >&5
/bin/ld: cannot find -lmkl_gf_lp64
/bin/ld: cannot find -lmkl_gnu_thread
/bin/ld: cannot find -lmkl_core

========

I realise there isn't "libmkl_gf_lp64.so" in /opt/intel directory, which I learn is "LP64 interface library for the GNU Fortran compilers"

To build R with Intel MKL, I wonder if I need to buy Intel fortran compiler to have the libmkl_gf_lp64.so library.

thanks,

Re:Building R with MKL

GouthamK_Intel — Thu, 11 Mar 2021 11:00:13 GMT

Hi Samuel,

Could you please go to /opt/intel/<composer_xe_XXXX>/mkl/lib/intel64

to see if you have the libmkl_gf_lp64.a and libmkl_gf_lp64.so in the directory? if no, then you may need to reinstall MKL.

If you have only libmk_gf_lp64.a, then please use the static link (Option C)as shown in the article.

https://software.intel.com/content/www/us/en/develop/articles/using-intel-mkl-with-r.html

Please revert to us once you check the above-mentioned details.

Regards

Goutham

Re: Re:Building R with MKL

syk — Tue, 16 Mar 2021 07:46:51 GMT

Hello Goutham,

Thank you for your help.

Yes. I eventually install psxe cluster linux 2017update 8 and found libmkl_gf_lp64.a and libmkl_gf_lp64.so installed.

I did not know at the first place "-lmkl_gf_lp64" does need interface library for gnu fortran. Now I learnt it.

BTW, I wonder why this R configure script don't return "LAPACK(MKL)" at the "External libraries: .." line. I can make R without any error and sure that BLAS (MKL) is fine.

But I am not sure if R lapack library is linked to MKL lapack.

====

$ ./configure CC=/usr/local/bin/gcc-10 CXX=/usr/local/bin/g++-10 --with-blas="-L/opt/intel/compilers_and_libraries_2017.8.262/linux/mkl/lib/intel64_lin -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm" --with-lapack --enable-R-profiling --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --enable-java --enable-long-double --with-readline --with-pcre1 --with-tcltk --with-cairo --with-libpng --with-jpeglib --with-libtiff --with-ICU --with-x

...

R is now configured for x86_64-pc-linux-gnu

Source directory: .
Installation directory: /usr/local

C compiler: /usr/local/bin/gcc-10 -g -O2
Fortran fixed-form compiler: gfortran -g -O2

Default C++ compiler: /usr/local/bin/g++-10 -std=gnu++11 -g -O2
C++14 compiler: /usr/local/bin/g++-10 -std=gnu++14 -g -O2
C++17 compiler: /usr/local/bin/g++-10 -std=gnu++17 -g -O2
C++20 compiler: /usr/local/bin/g++-10 -std=gnu++20 -g -O2
Fortran free-form compiler: gfortran -g -O2
Obj-C compiler:

Interfaces supported: X11, tcltk
External libraries: pcre1, readline, BLAS(MKL), curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared R library, shared BLAS, R profiling, memory profiling

Capabilities skipped:
Options not enabled:

Recommended packages: yes

=========

Re:Building R with MKL

GouthamK_Intel — Wed, 24 Mar 2021 07:52:19 GMT

Hi Samuel,

We are working on your issue internally, we will get back to you soon.

Regards

Goutham

Re:Building R with MKL

Khang_N_Intel — Wed, 28 Apr 2021 22:43:05 GMT

Hi Samuel,

Have you tried the R command sessionInfo()?

> sessionInfo()

If R is linked to MKL correctly you will see something like this:

R version....

...

Matrix products: default

BLAS/LAPACK: /optintel/oneapi/mkl/2021.2.0/lib/intel64/libmkl_rt.so.1

...

locale:

...

Best,

Khang

Re:Building R with MKL

Khang_N_Intel — Thu, 29 Apr 2021 01:08:26 GMT

Sorry, typo:

It should be something like this:

R version....

...

Matrix products: default

BLAS/LAPACK: /opt/intel/oneapi/mkl/2021.2.0/lib/intel64/libmkl_rt.so.1

...

locale:

...