On my RHEL-server I do not have admin rights, but I can create Conda environments. I would like to create a Conda environment running R with Intel MKL (Intel® Math Kernel Library).
I create the environment with R_defaults.yml, running $> conda env create --file R_defaults.yml:
name: R_defaults
channels:
- defaults
- conda-forge
dependencies:
- pkgs/r::r-essentials=3.6.0=r36_0
Activating the environment, starting R, and sessionInfo() I get that MKL is not used:
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.7 (Maipo)
Matrix products: default
BLAS/LAPACK: /home/geiringe/miniconda3/envs/R_r/lib/R/lib/libRblas.so
Microsoft R Open (https://mran.microsoft.com/download) can be installed with MKL.
It seems Anaconda has changed opinions about Microsoft R Open. In June 2018 it was said to become default R for the Anaconda distribution (https://www.anaconda.com/introducing-microsoft-r-open-as-default-r-for-anaconda-distribution/). Now they want us to migrate away from Microsoft R Open, and they will not update MRO packages (https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/#switch-an-environment-from-r-to-mro). The latest version of r::mro-base is 3.5.1, and is more than 1 year old. The latest version of r::r-essentials is 3.6.0
Is there a way for me to create a Conda environment with an updated version of R and with MKL?
The Anaconda r channel has been not updated in years - do not use it. Conda R users should use Conda Forge as their priority channel. To specify a BLAS/LAPACK variant, one can use the blas metapackage. The following YAML implements these recommendations:
r_mkl.yaml
name: r_mkl
channels:
- conda-forge
- defaults
dependencies:
- r-base=4.2 ## specify desired R version
- r-essentials
- blas=*=*mkl*
which can then be used like:
conda create -n r42_mkl -f r_mkl.yaml
Running this on osx-64, the output from R -e "sessionInfo()" in the activated environment shows:
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS/LAPACK: /Users/mfansler/miniconda3/envs/r42_mkl/lib/libmkl_rt.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2
This should behave very similarly on linux-64.