3 Install R for Oracle Machine Learning for R on On-Premises Oracle Database

This chapter explains how to install R for OML4R on On-Premises Oracle Database.

This chapter contains these topics:

3.1 About R and Oracle Machine Learning for R for On-Premises Database

OML4R requires an installation of R on the server computer and on each client computer that interacts with the server.

R is third-party, open source software. Open source R is governed by GNU General Public License (GPL) and not by Oracle licensing.

Note:

The version of R must be the same on the server and on each client computer. Also, the version of OML4R must be the same on the server and on each client computer.

3.1.1 About ROracle

ROracle is an open source R package that enables interaction between R and an Oracle database.

ROracle is maintained and supported by Oracle.

ROracle is one of the open source supporting packages that is used by Oracle Machine Learning for R. The supporting packages are introduced in Client and Server Components of Oracle Machine Learning for R for On-Premises Database and described in Table 6-2.

3.1.2 Oracle R Distribution and OML4R

Oracle recommends that you use Oracle R Distribution, Oracle's free distribution of R, with OML4R.

Oracle R Distribution offers significant advantages for OML4R.

Why Oracle R Distribution?

  • Oracle R Distribution simplifies the installation of R for OML4R.

  • Oracle R Distribution is supported by Oracle for customers of Oracle Machine Learning, Oracle Linux, and Oracle Big Data Appliance.

  • On Linux, Oracle R Distribution simplifies integration with the Intel Math Kernel Library (MKL). MKL greatly improves the performance of many mathematical computations in R, including highly vectorized and threaded Linear Algebra, Fast Fourier Transforms (FFT), Vector Math, and Statistics functions. (See Enable MKL Support for Oracle R Distribution on a Linux Client.)

3.2 Install Oracle R Distribution on Linux

Instructions for installing Oracle R Distribution on Oracle Linux and on Redhat Enterprise Linux.

Before you begin the installation, verify that your Linux version is supported by Oracle Machine Learning for R, as described in the table of platform requirements in Oracle Machine Learning for R System Requirements for On-Premises Database. You can use this command to verify the Linux version:

# uname -r

Note:

For Oracle Linux systems that have access to the internet, Oracle recommends installing Oracle R Distribution from the Oracle Linux Yum Server.

The following topics describe installing Oracle R Distribution:

3.2.1 Install Oracle R Distribution on Oracle Linux 8 Using Yum or Dnf

Oracle recommends using dnf to install Oracle R Distribution on Linux 8.

Yum simplifies the installation of Oracle R Distribution by automatically resolving RPM dependencies. If you install the RPMs directly, then you must resolve dependencies manually.

To install Oracle R Distribution on Oracle Linux 8 Using Yum or Dnf:

  1. Log in to the Linux server as root and change to the /etc/yum.repos.d directory:

    # cd /etc/yum.repos.d
  2. Use dnf to install the Oracle Linux 8 yum repository:

    dnf install oraclelinux-release-el8

    The repository oracle-linux-ol8.repo will be saved in /etc/yum.repos.d.

  3. For Oracle Linux 8, in addition to the Oracle Linux 8 main repository, the appstream, codereadybuilder, and addons repositories are required. Open oracle-linux-ol8.repo in a text editor and specify enabled=1 for ol8_baseos_latest, o18_appstream, o18_ codereadybuilder and ol8_addons:
    • Locate the section for baseos_latest repository and change enabled=0 to enabled=1.

      [ol8_baseos_latest]
      enabled=1

      The result will look similar like the following:

      [ol8_baseos_latest]
      name=Oracle Linux $releasever BaseOS ($basearch)
      baseurl=https://yum.oracle.com/repo/OracleLinux/OL8/baseos/latest/$basearch
      gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle
      gpgcheck=1
      enabled=1
    • Locate the section for appstream repository and change enabled=0 to enabled=1.

      [ol8_appstream]
      enabled=1

      The result will look similar like the following:

      [ol8_appstream]
      name=Oracle Linux $releasever Application Stream ($basearch)
      baseurl=https://yum.oracle.com/repo/OracleLinux/OL8/appstream/$basearch
      gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle
      gpgcheck=1
      enabled=1
    • Locate the section for codereadybuilder repository and change enabled=0 to enabled=1.

      [ol8_codereadybuilder]
      enabled=1

      The result will look similar like the following:

      [ol8_codereadybuilder]
      name=Oracle Linux $releasever Code Ready Builder ($basearch)
      baseurl=https://yum.oracle.com/repo/OracleLinux/OL8/codeready/builder/$basearch
      gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle
      gpgcheck=1
      enabled=1
    • Locate the section for addons repository and change enabled=0 to enabled=1.

      [ol8_addons]
      enabled=1

      The result will look similar like the following:

      [ol8_addons]
      name=Oracle Linux $releasever Add ons ($basearch)
      baseurl=https://yum.oracle.com/repo/OracleLinux/OL8/addons/$basearch/
      gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle
      gpgcheck=1
      enabled=1
  4. As root, install R-4.0.5 for Linux 8 using the dnf command. Execute the dnf command to install R.
    # dnf install R-4.0.5
    .

Note:

In newer Oracle Linux versions, the yum package manager has been replaced by dnf package manager.

3.2.2 Install Oracle R Distribution on Oracle Linux 7 Using Yum

Oracle recommends using yum to install Oracle R Distribution on Linux 7.

Yum simplifies the installation of Oracle R Distribution by automatically resolving RPM dependencies. If you install the RPMs directly, then you must resolve dependencies manually.

To install Oracle R Distribution on Oracle Linux 7 Using Yum:

  1. Log in to the Linux server as root and change to the /etc/yum.repos.d directory:

    # cd /etc/yum.repos.d
  2. List the contents of the directory to determine if the Oracle Linux 7 yum configuration file is present. The name of the configuration file is public-yum-ol7.repo.

    If the Oracle Linux 7 yum configuration file is not present, then download it from Oracle public yum by executing the wget command for your Linux platform:

    # wget https://public-yum.oracle.com/public-yum-ol7.repo
  3. Open public-yum-ol7.repo in a text editor and specify enabled=1 for ol7_latest, ol7_addons and ol7_optional_latest:

    [ol7_latest]
    enabled=1
    
    [ol7_addons]
    enabled=1
    
    [ol7_optional_latest]
    enabled = 1

    The location of the Oracle R Distribution packages is specified in ol7_addons. The location of the dependencies for the Oracle R Distribution RPMs is specified in ol7_latest and several dependencies are in optional_latest.

    The URLs for the Oracle R Distribution RPMs in the addons repository are shown in the example at the end of this topic.

    Note:

    If you are not using the most recent version of Oracle Linux and you want to install dependent packages that are specific to your version, then you must enable the corresponding Oracle Linux repository.

    For example, to enable the Oracle Linux 7 base repository open public-yum-ol7.repo in a text editor and specify enabled=1 for ol7_latest:

    
    [ol7_base]
    enabled=1

    The output will look similar to the following:

    [ol7_base]
    name=Oracle Linux $releasever installation media copy ($basearch)
    baseurl=https://public-yum.oracle.com/repo/OracleLinux/OL7/
    base/$basearch/
    gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle
    gpgcheck=1
    enabled=1
  4. Execute the yum install command to install R. Specify the version number to install for Rversion. For example, to install R-3.6.1, use the command yum install R-3.6.1.

    # yum install R-Rversion

    To install the most recent version of R that is available on Oracle public yum:

    # yum install R.x86_64

    Note:

    Do not assume that the most recent version of R on Oracle public yum is supported by your version of Oracle Machine Learning for R. Consult the table of configuration requirements and server support in Oracle Machine Learning for R System Requirements for On-Premises Database to determine which version of R you should use.

3.2.3 Install Oracle R Distribution on Oracle Linux Using RPMs

If yum is not available due to lack of internet access, then you can install the RPMs directly and resolve the dependencies manually.

However, Oracle recommends that you use yum to install Oracle R Distribution, because yum automatically resolves RPM dependencies.

To download and install the RPMs, log in as root and execute the command rpm -Uvh rpm_name for each RPM listed in the following sections:

3.2.3.1 Oracle R Distribution 4.0.5 RPMs for Oracle Linux 8

Lists the Oracle R Distribution RPMs for Oracle Linux 8.

The Oracle R Distribution RPMs for Oracle Linux 8 are listed as follows:

https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/R-4.0.5-1.0.1.el8.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/R-core-4.0.5-1.0.1.el8.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/R-devel-4.0.5-1.0.1.el8.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/libRmath-4.0.5-1.0.1.el8.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/libRmath-devel-4.0.5-1.0.1.el8.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL8/addons/x86_64/getPackage/libRmath-static-4.0.5-1.0.1.el8.x86_64.rpm
3.2.3.2 Oracle R Distribution 4.0.5 RPMs for Oracle Linux 7

Lists the Oracle R Distribution RPMs for Oracle Linux 7.

The Oracle R Distribution RPMs for Oracle Linux 7 are listed as follows:

https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-4.0.5-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-core-4.0.5-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-devel-4.0.5-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-4.0.5-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-devel-4.0.5-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-static-4.0.5-1.el7.x86_64.rpm
3.2.3.3 Oracle R Distribution 3.6.1 RPMs for Oracle Linux 7

Lists the Oracle R Distribution RPMs for Oracle Linux 7.

The Oracle R Distribution RPMs for Oracle Linux 7 are listed as follows:

https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-3.6.1-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-core-3.6.1-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-devel-3.6.1-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-3.6.1-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-devel-3.6.1-1.el7.x86_64.rpm
https://yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-static-3.6.1-1.el7.x86_64.rpm
3.2.3.4 Oracle R Distribution 3.3.0 RPMs for Oracle Linux 7

Lists the Oracle R Distribution RPMs for Oracle Linux 7.

The Oracle R Distribution RPMs for Oracle Linux 7 are listed as follows:

https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-core-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-core-extra-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/R-devel-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-devel-3.3.0-2.el7.x86_64.rpm
https://public-yum.oracle.com/repo/OracleLinux/OL7/addons/x86_64/getPackage/libRmath-static-3.3.0-2.el7.x86_64.rpm

3.2.4 Install Oracle R Distribution on Red Hat Enterprise Linux

Instructions on rebuilding the Oracle R Distribution RPMs on a Red Hat Linux system.

The Oracle Linux RPMs can be installed on Red Hat Linux systems. However, if you want to rebuild the Oracle R Distribution RPMs on a Red Hat Linux system, follow these instructions.

To install Oracle R Distribution on Red Hat Enterprise Linux:

  1. Create an RPM build directory structure:

    mkdir -p /rpmbuild/{BUILD,RPMS,SOURCES,SPECS,SRPMS}
    
  2. Set up RPM tools to use your own build tree (to avoid root):

    echo '%_topdir %(echo $HOME)/rpmbuild' > /.rpmmacros
    
  3. From Oracle public yum, download the source RPM (Rversion.olx.src.rpm where Rversion is the R version you are using and x is the Oracle Linux version you are using).

    Save the source RPM to the rpmbuild/SRPMS directory.

  4. Rebuild Red Hat Enterprise Linux using rpmbuild.

    rpmbuild --rebuild /rpmbuild/SRPMS/R-Rversion.elx.src.rpm

    Note:

    If any dependencies are missing, install them as root.

    The binary RPMs are built and saved under /rpmbuild/RPMS.

  5. Log in as root and execute these commands to install R:

    # rpm -i path/rpmbuild/RPMS/R-Rversion.olx.x86_64.rpm 
    # rpm -i path/rpmbuild/RPMS/R-core-Rversion.olx.x86_64.rpm 
    # rpm -i path/rpmbuild/RPMS/libRmath-Rversion.olx.x86_64.rpm 
    # rpm -i path/rpmbuild/RPMS/libRmath-devel-Rversion.olx.x86_64.rpm 
    # rpm -i path/rpmbuild/RPMS/libRmath-static-Rversion.olx.x86_64.rpm 
    # rpm -i path/rpmbuild/RPMS/R-devel-Rversion.olx.x86_64.rpm
    

    For example, this command installs R-4.0.5 on Red Hat Enterprise Linux x86-64 version 7, where the path to rpmbuild is /user/home/.

    rpm -i /user/home/rpmbuild/RPMS/x86_64/R-core-4.0.5-1.el7.x86_64.rpm

3.3 Configure Oracle R Distribution to Use MKL on the Client

Instructions for configuring Oracle R Distribution to use MKL on a Linux client.

With this simple configuration step, Oracle R Distribution dynamically uses MKL if it is installed on your system.

This topic contains these sections:

3.3.1 Enable MKL Support for Oracle R Distribution on a Linux Client

Follow these steps to enable MKL for Oracle R Distribution on a Linux Client.

  1. Install MKL. You can download MKL from the Intel® Math Kernel Library website.

    Note: To install MKL on your computer, you must have an MKL license.

  2. Add libmkl_rt.so, $RHOME/lib, and $ORACLE_HOME/lib to the LD_LIBRARY_PATH system environment variable. For example, in the Bash shell:

    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:
                             /path_to/libmkl_rt.so:
                             ${RHOME}/lib:
                             ${ORACLE_HOME}/lib
    
  3. Start R and execute the Sys.BlasLapack function:

    Sys.BlasLapack()
         $vendor
         [1] "Intel Math Kernel Library (Intel MKL)"
         $nthreads
         [1] -1
    

The returned value of $vendor indicates that MKL has replaced the BLAS and LAPACK that are native to R.

The returned value of nthreads indicates the number of threads to be used by MKL. By default all available threads are used ($nthreads= -1).

3.3.1.1 Modifying the Number of Threads for MKL on Linux

You can change the number of threads to be used by MKL by editing the system environment variable MKL_NUM_THREADS. For example, the following statement in the Bash shell, causes MKL to use 3 threads:

export MKL_NUM_THREADS=3

After setting MKL_NUM_THREADS to 3, the output of Sys.BlasLapack shows a value of 3 for $nthreads.

R> Sys.BlasLapack()
     $vendor
     [1] "Intel Math Kernel Library (Intel MKL)"
     $nthreads
     [1] 3

3.4 Uninstall Oracle R Distribution

Instructions for uninstalling Oracle R Distribution.

To uninstall Oracle R Distribution, follow the instructions in the following sections:

3.4.1 Uninstall Oracle R Distribution on Linux

Instructions for uninstalling Oracle R Distribution on Linux.

To uninstall Oracle R Distribution on Linux, log in as root and execute the commands in the example in the order shown. This example uninstalls R-4.0.5. To uninstall a different version of R, replace the R version in the example with the number of the version you want to uninstall.

Example 3-1 Linux Commands for Uninstalling Oracle R Distribution

Execute the rpm -e rpmname command, where rpmname is the name of the RPM you want to remove.

For example, to remove R-4.0.5 on Oracle Linux 7:

rpm -e R-4.0.5-1.el7 
rpm -e R-devel 
rpm -e R-core 
rpm -e R-core-extra 
rpm -e libRmath-devel 
rpm -e libRmath 
rpm -e libRmath-static