symlink MKL blas library for use by R

janackovski__atanas — Thu, 06 Sep 2018 12:36:25 GMT

Hi,

Can anyone please help me understand which .dylib to symlink for use by R on mac osx?

As an example I have used the following commands to try and link:

cd /Library/Frameworks/R.framework/Resources/lib

ln -sf /opt/intel/compilers_and_libraries_2018.3.185/mac/mkl/lib/libmkl_intel.dylib libRblas.dylib

I have tried symlinking various libraries, but still now joy. The error I when trying to run benchmark tests in R is:

dyld: Symbol not found: _MKL_Detect_Cpu_Global_Lock
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib
Command terminated abnormally.
        0.01 real         0.00 user         0.00 sys

I am using:

macOS 10.13.5
R version 3.5.1 (2018-07-02) \ Platform: x86_64-apple-darwin15.6.0 (64-bit)
RStudio Version 1.1.456

Please let me know if you need any further info. Any help would be greatly appreciated.

Thanks,

Atanas.

Hi Atanas,

Ying_H_Intel — Mon, 10 Sep 2018 08:00:46 GMT

Hi Atanas,

Please refer to : https://software.intel.com/en-us/articles/quick-linking-intel-mkl-blas-lapack-to-r

Best Regards,

Ying

and if you run into issue, please pay attention and DYLD_LIBRARY_PATH:

R uses GNU OpenMP multithread library libgomp.so, and Intel MKL uses Intel OpenMP multithread library, from Intel MKL 11.1.3 onwards, we provided the flexibility of supporting GNU threading layer by setting certain environment variables as explained in the MKL reference manual section here https://software.intel.com/en-us/node/528522/)

Please set the MKL interface and threading layer to GNU and LP64 as

$export MKL_INTERFACE_LAYER=GNU,LP64

$export MKL_THREADING_LAYER=GNU

topic symlink MKL blas library for use by R in Intel® oneAPI Math Kernel Library

symlink MKL blas library for use by R

Hi Atanas,