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This chapter describes the procedure for installing all required components prior to installing RUEI. The installation of the RUEI software itself is described in Chapter 2, 'Installing the Linux Operating System'.

Note:

It is assumed throughout this guide that the installation is performed as the root user, unless indicated otherwise.

3.1 Installing the Operating System Prerequisites

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  2. It's possible that the above module doesn't match the current version of Python, which is: 2.4.3 (#1, May 24 2008, 13:47:28) [GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] Can anyone shed some light on what I might be able to do to fix this?

  1. If the Enterprise Linux DVD is mounted automatically, the content is located in the directory /media/Enterprise Linux dvd 20090127 (the date depends on the downloaded version of the DVD). If the DVD is not automatically mounted, use the following commands to mount it:

    Note:

    In the rest of this chapter it is assumed the Linux operating system DVD is mounted on /mnt/dvd.

  2. Install all prerequisites for the Oracle database using the following commands:

  3. Issue the following command to install all prerequisites for the Apache Web server and PHP:

  4. Issue the following command to install all prerequisites for the SNMP and mail components. Note this step is optional, and only relevant to Reporter installations.

  5. Issue the following the commands to install all optional fonts. Alternatively, install the multi-byte character sets necessary to meet your NLS requirements.

  6. Continue with the rest of the installation procedure from Section 3.2.1, 'Creating the Database User Accounts and Groups'.

3.1.1 Installing All Requirements Using a Yum Repository (Optional)

As an alternative to manual installation, you can use a Yum repository to install the required RPMs. This requires a working Yum repository. For information on Yum repositories, see http://linux.duke.edu/projects/yum/. Install the necessary Oracle packages using the following commands:

Install the necessary RUEI packages using the following commands:

3.2 Installing and Configuring the Oracle Database

This section describes the procedure for installing the Oracle database.

Download Oracle Database 11g Release 1 (11.1.0.6.0) Standard Edition, Standard Edition One, and Enterprise Edition from the Oracle database home page (http://www.oracle.com/technology/software/products/database/index.html).

The procedure for installing the Oracle database is fully described in the product documentation. This section presents a summary of that procedure.

The information in this guide is based on the Oracle Database 11g for Linux x86-64 Quick Installation Guide. It is recommended that you download and review it. It is available at http://download.oracle.com/docs/cd/B28359_01/install.111/b32285/toc.htm.

Note:

The Oracle database's maximum memory usage is set by the MEMORY_TARGET parameter. By default, this is set to 40% of the available server RAM. For example, in a system with 16 GB RAM, it is set to approximately 6.4 GB. Note that if extra RAM is added to the server system to increase performance, it is not made available to the Oracle database until the MEMORY_TARGET parameter is manually increased.

Information about automatic memory management is available at http://download.oracle.com/docs/cd/B28359_01/server.111/b28310/memory003.htm#ADMIN11200.

3.2.1 Creating the Database User Accounts and Groups

  1. Create two groups (dba and oinstall) with the following commands:

  2. Create the oracle user, and specify oinstall as the primary group and dba as the secondary group, with the following command:

  3. Set the oracle user password with the following command:

3.2.2 Configuring the Kernel Parameter Settings

  1. Modify the /etc/sysctl.conf file to satisfy the Oracle installer's requirements by adding the following lines:

  2. Make these changes effective immediately with the following command:

3.2.3 Setting Shell Limits for the Oracle User

  1. To improve the performance of the software, you must increase the shell limits for the oracle user. Add the following lines to the /etc/security/limits.conf file:

  2. If not already present, add the following lines to the /etc/pam.d/login file:

  3. Depending on the oracle user's default shell, you need to make changes to it. For the Bourne, Bash, or Korn shell, add the following lines to the bottom of the /etc/profile file:

    For information about other shells, you should refer to the Oracle Database 11g Release 1 for Linux x86-64 Quick Installation Guide (at http://download.oracle.com/docs/cd/B28359_01/install.111/b32285/toc.htm).

3.2.4 Creating the Database Directory

Throughout this guide it is assumed that the directory /u01/app is the root of the Oracle installation. This is specified in the ORACLE_BASE environment variable.

  1. Enter the following command to display information about all mounted file systems:

    This command displays information about all the file systems mounted on the system, including:

    • The physical device name

    • The total amount, used amount, and available amount of disk space

    • The mount point directory for that file system

  2. Create the necessary subdirectories in the mount point directory that you identified and set the appropriate owner, group, and permissions for them using commands similar to the following:

3.2.5 Configuring the Oracle User's Environment

  1. Logon to the system as the oracle user.

  2. Add or edit the umask setting in the ~/.bash_profile file to the following:

  3. Make the setting active for the current shell by issuing the following command:

  4. Set the ORACLE_BASE environment variable to define the location of the root of the Oracle directory tree:

  5. Unzip the Oracle database installation zip file. This creates the directory database. Then, run the graphical installer (note this will not run under user root). Ensure that your X Window environment is properly set up. In addition, when logging on remotely with SSH, ensure X forwarding is enabled. Use the following commands:

  6. Use the installation wizard, and specify the values shown in Figure 3-1.

    Figure 3-1 Select Installation Method


    Description of 'Figure 3-1 Select Installation Method'

    Note that the Create Starter Database check box should be unchecked.

  7. When ready, click Next. Specify the values shown in Figure 3-2. When ready, click Next.

    Figure 3-2 Specify Inventory Directory and Credentials


    Description of 'Figure 3-2 Specify Inventory Directory and Credentials'

    Important:

    Any warnings or errors reported during database installation (especially any missing prerequisites) must be resolved before proceeding. See Section 3.1.1, 'Installing All Requirements Using a Yum Repository (Optional)' and Appendix A, 'Troubleshooting' for information about required components.

    If all dependencies are met, you can click Next.

  8. When installation is almost complete, you are prompted to run two scripts, orainstRoot.sh and root.sh, as root. This is shown in Figure 3-3.

    Figure 3-3 Configuration Scripts


    Description of 'Figure 3-3 Configuration Scripts'

    Run the two scripts indicated in Figure 3-3. They should be run in a terminal window as root. You will receive output similar to the following:

    The second script generates the following ouptut:

    On completion of each script, return the dialog shown in Figure 3-3, and click OK. In the main installer screen, verify that the message 'The installation of Oracle database 11g was successful' appears. Click Exit, and confirm by clicking Yes.

3.2.6 Creating an Oracle init Script File

  1. Logon as the root user.

  2. Create an /etc/init.d/oracledb script file to start and stop the Oracle database. An example of this initialization script is available in the RUEI installation zip file (/root/RUEI/50/oracledb) explained in Chapter 2, 'Installing the Linux Operating System'. Note that you will need to modify the settings for the ORACLE_BASE and ORACLE_HOME environment variables shown above if you selected a different installation directory for the Oracle database.

  3. Make the script file executable and use it to start the Oracle database with the following commands:

The Oracle database should now be up and running.

3.2.7 Setting the Memory Usage

For each Collector only system, set the available memory usage for the Oracle database to 10%. For example, if the system has 8 GB memory, then set the amount available to the Oracle database to 800 MB. To do so, issue the following commands as the oracle user:

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Note if you receive an error message stating the specified value is greater than MEMORY_MAX_TARGET, then the MEMORY_TARGET parameter has already been decreased.

Note that for Report systems, the default available memory usage setting does not need to be modified.

This chapter explains how to install R for Oracle R Enterprise. This chapter contains these topics:

See Also:

Chapter 5, 'Installing Oracle R Enterprise on Exadata'

3.1 About R and Oracle R Enterprise

Oracle R Enterprise 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.

See Also:

  • Table 1-2, 'Oracle R Enterprise Server Support Matrix' for the versions of R that are supported with Oracle R Enterprise

  • R Project for Statistical Computing at http://www.r-project.org

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 R Enterprise. The supporting packages are introduced in Section 1.2 and described in Table 6-2.

3.1.2 Oracle R Distribution and Oracle R Enterprise

Oracle recommends that you use Oracle R Distribution, Oracle's free distribution of R, with Oracle R Enterprise. Oracle R Distribution offers significant advantages for Oracle R Enterprise.

Why Oracle R Distribution?

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

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

  • On Windows and 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 Section 3.6, 'Configuring Oracle R Distribution to Use MKL on the Client'.)

  • On Oracle Solaris, Oracle R Distribution automatically uses Sun Performance Library. Like MKL for Linux and Windows, Sun Performance Library offers improved performance of many mathematical computations. Sun Performance Library is part of Oracle Solaris Studio.

3.1.3 Open Source R and Oracle R Enterprise

Although Oracle recommends that you use Oracle R Distribution whenever possible, you can use open source R with Oracle R Enterprise. If you choose to use open source R, then you must build it from source. Use the following configuration parameters:

See Also:

  • The R Installation and Administration manual for information about building R from source:

  • ”Using a Third-Party Package on the Client” in Oracle R Enterprise User's Guide

  • ”Installing a Third-Party Package for Use in Embedded R Execution” in Oracle R Enterprise User's Guide

3.2 Installing Oracle R Distribution on Linux

You can install 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 R Enterprise, as described in Table 1-1, 'Oracle R Enterprise Platform Requirements'.You can use this command to verify the Linux version:

Note:

For Oracle Linux systems that have access to the internet, Oracle recommends installing Oracle R Distribution from the Oracle public yum server at the following URL:

This topic contains these sections:

3.2.1 Installing Oracle R Distribution on Oracle Linux Using Yum

Oracle recommends that you use yum to install Oracle R Distribution. Yum simplifies the installation of Oracle R Distribution by automatically resolving RPM dependencies. If you install the RPMs directly as shown in Section 3.2.2, then you must resolve dependencies manually.

To install Oracle R Distribution on Oracle Linux Using Yum:

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

  2. List the contents of the directory to determine if the yum configuration file is present. The name of the configuration file is public-yum-xxx.repo, where xxx is either el5, for Oracle Linux 5, 0l6 for Oracle Linux 6, or 0l7, for Oracle Linux 7.

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

    or

    or

  3. Open public-yum-xxx.repo in a text editor and specify enabled=1 for xxx_latest and xxx_addons, where xxx indicates the version of Linux, either el5, ol6, or ol7:

    Also, for Oracle Linux 7 only:

    The location of the Oracle R Distribution packages is specified in xxx_addons. The location of the dependencies for the Oracle R Distribution RPMs is specified in xxx_latest. For Oracle Linux 7 only, several dependencies are in optional_latest.

    The URLs for the Oracle R Distribution RPMs in the addons repository are shown in Example 3-1. Specify 3.1.1-2 if Rversion is 3.1.1. Specify 3.0.1-2 if Rversion is 3.0.1.

    Example 3-1 Oracle R Distribution RPMs in addons Repository

    Oracle Linux 5:

    Oracle Linux 6:

    Oracle Linux 7:

    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 5.8 repository instead of the latest repository, follow these steps:

    1. Open the yum configuration file for Oracle Linux 5 in an editor.

    2. Locate the section for Oracle Linux 5, update 8.

    3. Change enabled=0 to enabled=1.

      The result looks like this:

  4. Execute the yum install command to install R. Specify 3.0.1 or 3.1.1 for Rversion

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

    Note:

    Do not assume that the most recent version of R on Oracle public yum is supported by your version of Oracle R Enterprise. Consult Table 1-2, 'Oracle R Enterprise Server Support Matrix' to determine which version of R you should use.

3.2.2 Installing Oracle R Distribution on Oracle Linux Using RPMs

Oracle recommends that you use yum to install Oracle R Distribution, because yum automatically resolves RPM dependencies. However, if yum is not available, then you can install the RPMs directly and resolve the dependencies manually.

To download and install the RPMs, log in as root and execute this command for each RPM listed in Section 3.2.2.1:

The Oracle R Distribution RPMs for R 3.1.1 and R 3.0.1 are listed in these topics:

3.2.2.1 Oracle R Distribution 3.1.1 RPMs for Oracle Linux 5

The Oracle R Distribution RPMs for Oracle Linux 5 are listed as follows:

If the dependent RPMs for Oracle Linux 5, listed in Section 3.2.2.2, are not automatically included, then download and install them explicitly.

3.2.2.2Oracle R Distribution 3.1.1 RPM Dependencies for Oracle Linux 5

The Oracle R Distribution dependent RPMs for Oracle Linux 5 are listed as follows:

3.2.2.3 Oracle R Distribution 3.1.1 RPMs for Oracle Linux 6

The Oracle R Distribution RPMs for Oracle Linux 6 are listed as follows:

If the following dependent RPM is not automatically included, then download and install it explicitly:

3.2.2.4 Oracle R Distribution 3.0.1 RPMs for Oracle Linux 5

The Oracle R Distribution RPMs for Oracle Linux 5 are listed as follows:

If the dependent RPMs for Oracle Linux 5, listed in Section 3.2.2.2, are not automatically included, then download and install them explicitly.

3.2.2.5Oracle R Distribution 3.0.1 RPM Dependencies for Oracle Linux 5

The Oracle R Distribution dependent RPMs for Oracle Linux 5 are listed as follows:

3.2.2.6 Oracle R Distribution 3.0.1 RPMs for Oracle Linux 6

The Oracle R Distribution RPMs for Oracle Linux 6 are listed as follows:

If the following dependent RPM is not automatically included, then download and install it explicitly:

3.2.3 Installing Oracle R Distribution on Red Hat Enterprise Linux

Tip:

Rversion represents the version of Oracle R Distribution. Replace Rversion with 3.1.1-2 for R 3.1.1; replace Rversion with 3.0.1-2 for R 3.0.1.

To install Oracle R Distribution on Red Hat Enterprise Linux 6:

  1. Create an RPM build directory structure:

  2. Set up RPM tools to use your own build tree (to avoid root):

  3. Download the source RPM (R-version.el6.src.rpm) from Oracle public yum.

    For Red Hat Enterprise Linux 6:

    http://public-yum.oracle.com/repo/OracleLinux/OL6/addons/x86_64/

    Save the source RPM to the rpmbuild/SRPMS directory.

  4. Rebuild Red Hat Enterprise Linux using rpmbuild.

    Note:

    • Linux 5

      The source RPM, R-3.1.1-2.el5.src.rpm, is here:

      http://public-yum.oracle.com/repo/EnterpriseLinux/EL5/addons/x86_64/

    • Linux 7

      The source RPM, R-3.1.1-2.el7.src.rpm, is here:

    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:

    For example, this command installs R 3.1.1 on Red Hat Enterprise Linux x86-64 version 6, where the path to rpmbuild is /refresh/home/.

3.3 Installing Oracle R Distribution on Oracle Solaris

You can install Oracle R Distribution on Oracle Solaris on Intel and on SPARC platforms. Before you begin the installation, verify that your Oracle Solaris version is supported by Oracle R Enterprise, as described in Table 1-1, 'Oracle R Enterprise Platform Requirements'.You can use this command to verify the version of Oracle Solaris:

To install Oracle R Distribution on Oracle Solaris:

  1. Go to the Oracle Open Source Software Download page for Oracle R Distribution:

  2. Download the files for your installation, where Rversion is 3.1.1-2 for R 3.1.1 or 3.0.1-2 for R 3.0.1:

    • For x86 64-bit systems:

    • For SPARC 64-bit systems:

  3. Uncompress the first file, either sol110-x86-64 or sol10-sparc.

  4. Run install.sh as root to install the Solaris PKG file for Oracle R Distribution.

  5. Uncompress the second file, either supporting-sol10-x86-64 or supporting-sol10-sparc, to a local directory such as $ORACLE_HOME/lib. Add that directory to $LD_LIBRARY_PATH.

    These tar files contain the shared libraries for libR.so:

    • libiconv.so.2

    • libncurses.so.5

    • libreadline.so.6

    • libsunperf.so

    libsunperf.so, Sun Performance Library, and its dependent shared libraries are included in Oracle Solaris Studio.

  6. Run the following command to verify that libR.so is picking up its shared library dependencies correctly from the local directory.

  7. Start R by typing R at the command prompt:

3.4 Installing Oracle R Distribution on IBM AIX

Before installing Oracle R Distribution, verify that your version of IBM AIX is supported by Oracle R Enterprise, as described in Table 1-1, 'Oracle R Enterprise Platform Requirements'.You can use this command to verify the version of IBM AIX:

To install Oracle R Distribution on IBM AIX:

  1. Go to the Oracle Open Source Software Download page for Oracle R Distribution:

  2. Download the files for your installation, where Rversion is 3.1.1.0 for R 3.1.1 or 3.0.1.0 for R 3.0.1:

  3. Uncompress and untar ord-supporting-aix.tar.gz:

    You can also download these RPMs from http://www.perzl.org/aix/.

  4. Install the RPMs as root using an rpm command:

    To upgrade existing dependencies, use:

    If you experience conflicts with dependencies, use:

  5. Add /opt/freeware/lib to the LIBPATH environment variable:

    • For ksh:

    • For csh:

    Ensure that /opt/freeware/lib is before /usr/lib.

  6. Uncompress ORD-Rversion-aix.bft.gz to get ORD-Rversion-aix.bff:

  7. To install all the filesets in Oracle R Distribution, execute the installp command (with the apply option) as root:

    You can also install independent filesets:

  8. Run ldd to ensure that shared library dependencies were picked up correctly:

  9. Add /usr/lib/R/lib to the LIBPATH environment variable:

    • For ksh:

    • For csh:

3.5 Installing Oracle R Distribution on Microsoft Windows

Before installing Oracle R Distribution, verify that your version of Microsoft Windows is supported by Oracle R Enterprise, as described in Table 1-1, 'Oracle R Enterprise Platform Requirements'.

Follow these steps to install Oracle R Distribution on Windows:

  1. Go to the Oracle Open Source Software Download page for Oracle R Distribution:

  2. Select R Distribution for Windows 64 bit. Save the zip file on your computer.

  3. Unzip the file and extract the executable file.

  4. Double click the executable file to start the installation of Oracle R Distribution.

  5. Follow the instructions to complete the installation.

3.6Configuring Oracle R Distribution to Use MKL on the Client

The instructions in this section explain how to configure Oracle R Distribution to use MKL on a Linux or Windows client. With this simple configuration step, Oracle R Distribution dynamically uses MKL if it is installed on your system.

This topic contains these sections:

3.6.1 Enabling 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 following 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:

  3. Start R and execute the Sys.BlasLapack function:

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).

3.6.1.1 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:

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

3.6.2 Enabling MKL Support for Oracle R Distribution on a Windows Client

Follow these steps to enable MKL for Oracle R Distribution on a Windows client (64-bit):

  1. Install MKL. You can download MKL from the following website:

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

  2. Add the location of libOrdBlasLoader.dll and mkl_rt.dll to the PATH system environment variable.For instructions, see.

    Note:

    In a typical installation of Oracle R Distribution 3.1.1, libOrdBlasLoader.dll is located in the R home directory:

    In a full installation of MKL 11.1, mkl_rt.dll is located in the Intel MKL Composer XE directory:

  3. Start R and execute the Sys.BlasLapack function:

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).

3.6.2.1 Modifying the Number of Threads for MKL on Windows

You can change the number of threads to be used by MKL by editing the system environment variable MKL_NUM_THREADS. If MKL_NUM_THREADS does not exist, then you must create it as described in:

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

3.7 Uninstalling Oracle R Distribution

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

3.7.1 Uninstalling Oracle R Distribution on Windows

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Uninstall Oracle R Distribution just as you would uninstall any other Windows program, using Programs and Features in Windows Control Panel.

3.7.2 Uninstalling Oracle R Distribution on Linux

To uninstall Oracle R Distribution on Linux, log in as root and execute these commands in this order. To uninstall a different version of R, replace 3.1.1 with the version number.

Example 3-2 Linux Commands for Uninstalling Oracle R Distribution

Execute the following commands as root. Specify the version of R for Rversion, for example 3.1.1 or 3.0.1.

3.7.3 Uninstalling Oracle R Distribution on Oracle Solaris

To uninstall Oracle R Distribution on Oracle Solaris, follow the instructions in the readme on the Oracle R Distribution download page on the Oracle Technology Network:

The Oracle R Distribution installation directory on Oracle Solaris includes an uninstall script. Log in as root and run the script as follows:

Example 3-3 Solaris Script for Uninstalling Oracle R Distribution

Execute this script as root:

3.7.4 Uninstalling Oracle R Distribution on IBM AIX

To uninstall Oracle R Distribution on IBM AIX, follow the instructions in the readme on the Oracle R Distribution download page on the Oracle Technology Network:

Example 3-4 AIX Scripts for Uninstalling Oracle R Distribution

To uninstall all filesets, execute this script as root:

To uninstall individual filesets, specify their names: