Skip to content

Corrections about MKL setup in R guide #50

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
david-cortes-intel wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Corrections about MKL setup in R guide #50

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 25 additions & 7 deletions software/R/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,19 +40,37 @@ It is highly recommended to use Intel's [oneMKL](https://www.intel.com/content/w

##### Linux

On Linux, by default, R will link to a generic `libblas` and `liblapack`. On Debian-based systems, the vendor version behind those can be controlled through the [Debian alternatives system](https://wiki.debian.org/DebianAlternatives). To set oneMKL as the system provider for `libblas` and `liblapack`, after installing it through [Intel's APT packages](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html?operatingsystem=linux&linux-install=apt), execute the following commands and choose oneMKL (`libmkl_rt.so`) as provider:
On Linux, by default, R will link to a generic `libblas` and `liblapack`. On **Debian**-based systems (including derivatives such as Ubuntu and Mint), the vendor version behind those can be controlled through the [Debian alternatives system](https://wiki.debian.org/DebianAlternatives). OneMKL can be set as the system provider for `libblas` and `liblapack` after installing it through [Intel's APT packages](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html?operatingsystem=linux&linux-install=apt):

* To install MKL:
```shell
sudo update-alternatives --config libblas.so-x86_64-linux-gnu
sudo update-alternatives --config liblapack.so-x86_64-linux-gnu
sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu # used by R 4.x
sudo update-alternatives --config liblapack.so.3-x86_64-linux-gnu # used by R 4.x
sudo apt install -y gpg-agent wget # prerequisites
wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt update
sudo apt install intel-oneapi-mkl
```

If oneMKL is installed through means other than APT, one might first need to [source its environment script](https://www.intel.com/content/www/us/en/docs/onemkl/developer-guide-linux/2026-0/setting-environment-variables.html#SETTING-ENVIRONMENT-VARIABLES) **before** executing the commands above:
* To add oneMKL's paths to system library loading paths, assuming version 2026.0 (not needed if one [sources the environment script](https://www.intel.com/content/www/us/en/docs/onemkl/developer-guide-linux/2026-0/setting-environment-variables.html#SETTING-ENVIRONMENT-VARIABLES) before launching R):
```shell
printf "/opt/intel/oneapi/2026.0/lib/\n/opt/intel/oneapi/mkl/latest/lib/\n" | sudo tee /etc/ld.so.conf.d/intel-oneapi-mkl.conf

@david-cortes-intel david-cortes-intel Aug 13, 2026

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@vmalia MKL packages that don't have 'runtime' in the name and which put files under /opt/intel/oneapi/mkl do not provide this file. I cannot think of any programmatic way to achieve this in a version-agnostic way given the paths that MKL uses.

Please review and provide alternatives if there are any.

sudo ldconfig
```

* To register oneMKL as a selectable system provider for BLAS and LAPACK:
```shell
sudo update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so libblas.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so 1 && \
sudo update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so liblapack.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so 1 && \
sudo update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so 1 && \
sudo update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so 1
```

* To set oneMKL as the system provider for BLAS and LAPACK:
```shell
source /opt/intel/oneapi/setvars.sh
sudo update-alternatives --set libblas.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so && \
sudo update-alternatives --set liblapack.so-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so && \
sudo update-alternatives --set libblas.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so && \
sudo update-alternatives --set liblapack.so.3-x86_64-linux-gnu /opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so
```

##### Windows
Expand Down