R - 4.1.3

Basic Information

  • Instalation Date: 18/03/2022
  • URL: https://www.r-project.org/
  • ** APolo Version** Apolo II
  • ** License:** https://www.r-project.org/Licenses/

Dependencies

  • zlib >= 1.25
  • bzip2 >= 1.0.6
  • xz
  • pcre2 >= 10.30
  • curl >= 7.28.0 with https support
  • JDK
  • mpi
  • mkl
  • OneApi compiler
  • lapack

Installation

After the dependencies have been resolved and configured, the R installation can start.

Note

The intel compiler will be used to build R

  1. Download the selected version from an official mirror (https://cran.r-project.org/mirrors.html).

    $ wget https://cran.r-project.org/src/base/R-4/R-4.1.3.tar.gz
$ tar xvzf R-4.1.3.tar.gz

  2. Load the corresponding modules to set the building environment.

    $ module load zlib/1.2.11_Intel_oneAPI-2022_update-1 bzip2/1.1.0_Intel_oneAPI-2022_update-1  xz/5.2.5_Intel_oneAPI-2022_update-1 pcre2/10.39_Intel_oneAPI-2022_update-1 curl/7.82.0_Intel_oneAPI-2022_update1
$ module load java/jdk-17.0.2 intel/2022_oneAPI-update1 mpi/2021.5.1 mkl/2022.0.2 lapack/3.10.0_Intel_oneAPI-2022_update-1

  3. Configure the resources

    ./configure --prefix=/share/apps/r/4.1.3/Intel_oneAPI-2022_update-1 \
--build=x86_64-redhat-linux --enable-R-shlib \
--with-blas="-L/share/apps/intel/oneAPI/2022_update-1/mkl/2022.0.2/lib/intel64 \
-lmkl_rt -liomp5 -lpthread" --with-lapack --enable-BLAS-shlib \
--without-x --enable-memory-profiling \
LDFLAGS="$LDFLAGS -qopenmp -L/share/apps/bzip2/1.1.0/Intel_oneAPI-2022_update-1/lib64 \
-L/share/apps/pcre2/10.39/Intel_oneAPI-2022_update-1/lib64 \
-L/share/apps/xz/5.2.5/Intel_oneAPI-2022_update-1/lib" \
CFLAGS="$CFLAGS -fPIC -qopenmp -O3 -ipo -xHost \
-I/share/apps/bzip2/1.1.0/Intel_oneAPI-2022_update-1/include \
-I/share/apps/pcre2/10.39/Intel_oneAPI-2022_update-1/include \
-I/share/apps/xz/5.2.5/Intel_oneAPI-2022_update-1/include" \
CXXFLAGS="$CXXFLAGS -fPIC -qopenmp -O3 -ipo -xHost \
-I/share/apps/bzip2/1.1.0/Intel_oneAPI-2022_update-1/include \
-I/share/apps/xz/5.2.5/Intel_oneAPI-2022_update-1/include" \
FFLAGS="$FFLAGS -fPIC -qopenmp -O3 -ipo -xHost" \
FCFLAGS="$FCFLAGS -fPIC -qopenmp -O3 -ipo -xHost" --with-readline=no

  4. Before doing make, delete or comment the following line on src/include/config.h.in

    #undef HAVE_MATHERR

  5. Build the sources

    $ make -j 16
$ make -j 16 install

Module

The following is the module used for this version.

#%Module1.0#####################################################################
##
## modules r/4.1.3_Intel_oneAPI-2022_update-1
##
## /share/apps/r/4.1.3/Intel_oneAPI-2022_update-1  Written by Bryan Lopez Parra
##

proc ModulesHelp { } {
    puts stderr "\tR/4.1.3_Intel_oneAPI-2022_update-1 - sets the Environment for R in \
    \n\tthe share directory /share/apps/r/4.1.3/Intel_oneAPI-2022_update-1\n"
}

module-whatis "\n\n\tSets the environment for R language \
            \n\tbuilt with  Intel MKL oneAPI 2022 (Update-1)version \
            \n\t(Update-1)\n"

# for Tcl script use only
set       topdir     /share/apps/r/4.1.3/Intel_oneAPI-2022_update-1
set       version    4.1.3
set       sys        x86_64-redhat-linux

conflict r

module load zlib/1.2.11_Intel_oneAPI-2022_update-1 bzip2/1.1.0_Intel_oneAPI-2022_update-1  xz/5.2.5_Intel_oneAPI-2022_update-1 pcre2/10.39_Intel_oneAPI-2022_update-1 curl/7.82.0_Intel_oneAPI-2022_update1
module load java/jdk-17.0.2 intel/2022_oneAPI-update1 mpi/2021.5.1 mkl/2022.0.2 lapack/3.10.0_Intel_oneAPI-2022_update-1

prepend-path    PATH                    $topdir/bin

prepend-path    LD_LIBRARY_PATH         $topdir/lib64/R/lib
prepend-path    LD_RUN_PATH             $topdir/lib64/R/lib
prepend-path    LIBRARY_PATH            $topdir/lib64/R/lib
prepend-path    LD_LIBRARY_PATH         $topdir/lib64/R/modules
prepend-path    LD_RUN_PATH             $topdir/lib64/R/modules
prepend-path    LIBRARY_PATH            $topdir/lib64/R/modules

prepend-path    C_INCLUDE_PATH          $topdir/lib64/R/include
prepend-path    CXX_INCLUDE_PATH        $topdir/lib64/R/include
prepend-path    CPLUS_INCLUDE_PATH      $topdir/lib64/R/include
prepend-path    C_INCLUDE_PATH          $topdir/lib64/R/include/R_ext
prepend-path    CXX_INCLUDE_PATH        $topdir/lib64/R/include/R_ext
prepend-path    CPLUS_INCLUDE_PATH      $topdir/lib64/R/include/R_ext

prepend-path    PKG_CONFIG_PATH         $topdir/lib64/pkgconfig

prepend-path    MAN_PATH                $topdir/share/man
Authors: