Build R 4.0 with MKL

[ixxmu]

Update: sessionInfo shows sucess, but still work as R regular! Maybe certain environment variables failure, please help!!!

Have tested, it worked！

Not responsible for solving problems, just Goolge it!

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)
Matrix products: default
BLAS:   /opt/biosoft/R/4.0.1/lib64/R/lib/libRblas.so
LAPACK: /opt/biosoft/R/4.0.1/lib64/R/lib/libRlapack.so
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
loaded via a namespace (and not attached):
[1] compiler_4.0.1 tools_4.0.1   

Outline 4 steps to do

• 1 Microsoft R MKL installed (latest 3.5.3)

• 2 R official installed (R 3.6.1)

• 4 Bulid R 4.0.1

• 3 Setup Rstudio Server

Start here

• Microsoft R MKL installed (latest 3.5.3)

  Microsoft R MKL Official Website

• R official installed (R 3.6.1)

  yum install R //based on your own system to install R for CentOS 8, here the guides

• Bulid R 4.0.1

  Intel MKL Official Guides Intel MKL On Linux Assume you have obtained R-4.0.1.tar.gz form CRAN source website

$ tar -xzvf R-4.0.1.tar.gz
$ cd R-4.0.1
$ ./configure --enable-R-shlib --prefix=/opt/xxx/R/4.0.1 --with-readline=yes --with-libpng=yes --with-readline=no --with-x=no
// **_--enable-R-shlib_  for rstudio server working, _--prefix=_ for location setting, you must set install your _R_ in _opt_ or sub except you are a Rstudio Server Pro user**
$ make
$ ldd bin/exec/R
(To make sure it will link libRblas.so although it may show that libRblas.so => not found , 
if is all right, just _sudo make install_  )
$ find / -name libRblas.so
$ cd & vi .bashrc
_export LD_LIBRARY_PATH="R-install-location/lib65/R/lib:$LD_LIBRARY_PATH"_
$ cd R-4.0.1
$ ldd bin/exec/R
$ sudo make install

type $ /opt/xxx/R/4.0.1/bin/R in your terminal, if all steps work, you will get new R with MKL specified. $ SessionInfo()

• Setup Rstudio Server

  vi /etc/rstudio/rserver.conf
  rsession-which-r=**/opt/biosoft/R/4.0.1/bin/R**
  note your own R install location, ensure here right
  systemctl stop studio-server
  sudo rstudio-server verify-installation  
  // may happen some problems, you can find the error info here
  systemctl restart rstudio-server
  systemctl status rstudio-server

  Enjoy your latest R with MKL integration !

[ixxmu]

sessionInfo shows sucess, but still work with R regular! Maybe certain environment variables failure, please help!!!

m <- 10000 n <- 2000 A <- matrix (runif (m*n),m,n) system.time (S <- svd (A,nu=0,nv=0))

[dazhwu]

According to your session info, your R is base R and is not using MKL. “BLAS: /opt/biosoft/R/4.0.1/lib64/R/lib/libRblas.so LAPACK: /opt/biosoft/R/4.0.1/lib64/R/lib/libRlapack.so”

Check this: https://github.com/alexisph/high_performance_r

[ixxmu]

According to your session info, your R is base R and is not using MKL. “BLAS: /opt/biosoft/R/4.0.1/lib64/R/lib/libRblas.so LAPACK: /opt/biosoft/R/4.0.1/lib64/R/lib/libRlapack.so”

Check this: https://github.com/alexisph/high_performance_r

yes, i found the problem and then rebuild latest-R with intel MKL on CentOS 7

R version 4.0.1 (2020-06-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /opt/intel/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

[mmekarnia]

Hi Guys

I have the same issue that ixxmu described above .I see that he already fixed his issue but its not clear to me how he did it. I need help.

In my case i have R 3.6.3 that was build outside the box using docker and brought to the server because of root restrictions .The mkl is configured on this version and multithreading is working fine see below.

sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default BLAS/LAPACK: /app/r/lib64/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.6.3 tools_3.6.3

I build a new version R4.1.1 but the mkl multithreading is not working see below.

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default BLAS: /app/R4/lib64/R/lib/libRblas.so LAPACK: /app/R4/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1