This chapter explains how to install R for Oracle R Enterprise. This chapter contains these topics:
Note:
Instructions for installing Oracle R Distribution on Exadata are in Chapter 5.Oracle R Enterprise requires an installation of R on the computer that hosts Oracle R Enterprise Server and on each computer that hosts an Oracle R Enterprise client. If you intend to use both client and server components of Oracle R Enterprise directly on the server, then only one installation of R is necessary.
See Also:
Table 1-2, "Oracle R Enterprise Server Support Matrix" for the versions of R that are supported with Oracle R Enterprise
Oracle recommends that you use Oracle R Distribution with Oracle R Enterprise whenever possible. Oracle R Distribution offers these advantages:
Oracle R Distribution is compiled with the flags that are required by Oracle R Enterprise server components.
On Linux and Windows platforms, Oracle R Distribution integrates seamlessly with the Intel Math Kernel Library (MKL) to provide high performance mathematical computations.
On Solaris platforms, Oracle R Distribution automatically uses Sun Performance Library to provide high performance mathematical computations.
Oracle provides support for Oracle R Distribution with Oracle R Enterprise.
You can use open source R with Oracle R Enterprise. Use the following R configuration parameters to build it from source:
./configure --with-lapack --with-ICU=no --enable-R-shlib
See Also:
The R Installation and Administration manual for information about building R from source:Oracle recommends that you use the Oracle public yum server for installing R on Linux. Oracle public yum is located at the following URL:
http://public-yum.oracle.com/
These topics explain how to install Oracle R Distribution on Linux systems:
Note:
Before installing Oracle R Distribution, verify that your version of Oracle Linux is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".You can use this command to verify the Linux version:
% uname -r
To install Oracle R Distribution on Oracle Linux Using Yum:
Log in to the Linux server as root and change to the /etc/yum.repos.d directory:
# cd /etc/yum.repos.d
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, or 0l6, for Oracle Linux 6.
If the yum configuration file is not present, then download it from Oracle public yum by executing the wget command for your Linux platform:
# wget http://public-yum.oracle.com/public-yum-el5.repo
or
# wget http://public-yum.oracle.com/public-yum-ol6.repo
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 or ol6:
[xxx_latest] enabled=1 [xxx_addons] enabled=1
The Oracle R Distribution packages reside in xxx_addons. The dependencies for the Oracle R Distribution RPMs reside in the latest Oracle Linux repository, xxx_latest.
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:Open the yum configuration file for Oracle Linux 5 in an editor.
/etc/yum.repos.d/public-yum-el5.repo
Locate the section for Oracle Linux 5, update 8.
[ol5_u8_base]
Change enabled=0 to enabled=1.
The result looks like this:
[ol5_u8_base] name=Oracle Linux $releasever Update 8 installation media copy ($basearch) baseurl=http://public-yum.oracle.com/repo/OracleLinux/OL5/8/ base/$basearch/ gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-oracle gpgcheck=1 enabled=1
Execute the yum install command to install R.
To install R-3.0.1:
# yum install R-3.0.1
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 R Enterprise. Consult Table 1-2, "Oracle R Enterprise Server Support Matrix" to determine which version of R you should use.Oracle recommends that you use yum to install Oracle R Distribution. However, if yum is not available, you can install Oracle R Distribution using RPMs.
Note:
Before installing Oracle R Distribution, verify that your version of Oracle Linux is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".You can use this command to verify the Linux version:
% uname -r
To download and install the RPMs, log in as root and execute this command for each RPM listed in Section 3.2.2.1:
# rpm -Uvh rpm_name
The Oracle R Distribution 3.0.1 RPMs are listed in these topics:
The Oracle R Distribution RPMs for Oracle Linux 5 are listed as follows:
R-2.15.3-1.el5.x86_64.rpm R-core-2.15.3-1.el5.x86_64.rpm R-devel-2.15.3-1.el5.x86_64.rpm libRmath-2.15.3-1.el5.x86_64.rpm libRmath-devel-2.15.3-1.el5.x86_64.rpm
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.
The Oracle R Distribution dependent RPMs for Oracle Linux 5 are listed as follows:
atk-1.12.2-1.fc6.x86_64.rpm avahi-0.6.16-10.el5_6.x86_64.rpm avahi-compat-libdns_sd-0.6.16-10.el5_6.x86_64.rpm bitstream-vera-fonts-1.10-7.noarch.rpm bzip2-devel-1.0.3-6.el5_5.x86_64.rpm cairo-1.2.4-5.el5.x86_64.rpm chkfontpath-1.10.1-1.1.x86_64.rpm cpp-4.1.2-54.el5.x86_64.rpm cups-1.3.7-30.el5_9.3.x86_64.rpm cups-libs-1.3.7-30.el5_9.3.x86_64.rpm dbus-python-0.70-9.el5_4.x86_64.rpm desktop-file-utils-0.10-7.x86_64.rpm dialog-1.0.20051107-1.2.2.x86_64.rpm ed-0.2-39.el5_2.x86_64.rpm gcc-4.1.2-54.el5.x86_64.rpm gcc-c++-4.1.2-54.el5.x86_64.rpm gcc-gfortran-4.1.2-54.el5.x86_64.rpm ghostscript-8.70-14.el5_8.1.x86_64.rpm ghostscript-fonts-5.50-13.1.1.noarch.rpm gmp-4.1.4-10.el5.x86_64.rpm gtk2-2.10.4-29.el5.x86_64.rpm hicolor-icon-theme-0.9-2.1.noarch.rpm libFS-1.0.0-3.1.x86_64.rpm libX11-1.0.3-11.el5_7.1.x86_64.rpm libX11-devel-1.0.3-11.el5_7.1.x86_64.rpm libXau-devel-1.0.1-3.1.x86_64.rpm libXdmcp-devel-1.0.1-2.1.x86_64.rpm libXfont-1.2.2-1.0.4.el5_7.x86_64.rpm libfontenc-1.0.2-2.2.el5.x86_64.rpm libgcc-4.1.2-54.el5.i386.rpm libgcc-4.1.2-54.el5.x86_64.rpm libgfortran-4.1.2-52.el5_8.1.i386.rpm libgfortran-4.1.2-54.el5.x86_64.rpm libstdc++-4.1.2-54.el5.i386.rpm libstdc++-4.1.2-54.el5.x86_64.rpm libstdc++-devel-4.1.2-54.el5.i386.rpm libstdc++-devel-4.1.2-54.el5.x86_64.rpm libtiff-3.8.2-18.el5_8.x86_64.rpm mesa-libGL-6.5.1-7.11.el5_9.x86_64.rpm mesa-libGL-devel-6.5.1-7.11.el5_9.x86_64.rpm netpbm-10.35.58-10.el5.x86_64.rpm netpbm-progs-10.35.58-10.el5.x86_64.rpm pango-1.14.9-8.0.1.el5_7.3.x86_64.rpm paps-0.6.6-20.el5.x86_64.rpm pcre-6.6-6.el5_6.1.x86_64.rpm pcre-devel-6.6-6.el5_6.1.x86_64.rpm poppler-0.5.4-19.el5.x86_64.rpm poppler-utils-0.5.4-19.el5.x86_64.rpm tcl-8.4.13-6.el5.x86_64.rpm tcl-devel-8.4.13-6.el5.x86_64.rpm tetex-3.0-33.15.el5_8.1.x86_64.rpm tetex-dvips-3.0-33.15.el5_8.1.x86_64.rpm tetex-fonts-3.0-33.15.el5_8.1.x86_64.rpm tetex-latex-3.0-33.15.el5_8.1.x86_64.rpm texinfo-4.8-14.el5.x86_64.rpm texinfo-tex-4.8-14.el5.x86_64.rpm tk-devel-8.4.13-5.el5_1.1.x86_64.rpm ttmkfdir-3.0.9-23.el5.x86_64.rpm urw-fonts-2.3-6.1.1.noarch.rpm xorg-x11-font-utils-7.1-3.x86_64.rpm xorg-x11-proto-devel-7.1-13.el5.x86_64.rpm xorg-x11-xfs-1.0.2-5.el5_6.1.x86_64.rpm zlib-1.2.3-7.el5.i386.rpm zlib-1.2.3-7.el5.x86_64.rpm zlib-devel-1.2.3-7.el5.x86_64.rpm
The Oracle R Distribution RPMs for Oracle Linux 6 are listed as follows:
R-3.0.1-2.el6.x86_64.rpm R-core-3.0.1-2.el6.x86_64.rpm R-devel-3.0.1-2.el6.x86_64.rpm libRmath-3.0.1-2.el6.x86_64.rpm libRmath-devel-3.0.1-2.el6.x86_64.rpm
If the following dependent RPM is not automatically included, then download and install it explicitly.
texinfo-tex-4.13a-8.el6.x86_64.rpm
Note:
Before installing Oracle R Distribution, verify that your version of Red Hat Enterprise Linux is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".You can use this command to verify the Linux version:
% uname -r
The following installation instructions are specific to Red Hat Enterprise Linux 6. For Red Hat Enterprise Linux 5, change ol6 to el5.
To install Oracle R Distribution on Red Hat Enterprise Linux 6:
Create an RPM build directory structure:
% mkdir -p /rpmbuild/{BUILD,RPMS,SOURCES,SPECS,SRPMS}
Set up RPM tools to use your own build tree (to avoid root login):
% echo '%_topdir %(echo $HOME)/rpmbuild' > /.rpmmacros
Download the source RPMs (*.src.rpm) from Oracle public yum. For Red Hat Enterprise Linux 6:
http://public-yum.oracle.com/repo/OracleLinux/OL6/
Save the source RPMs to the rpmbuild/SRPMS directory.
Rebuild Red Hat Enterprise Linux using rpmbuild.
% rpmbuild --rebuild /rpmbuild/SRPMS/R-3.0.1-1.el6.src.rpm
Note:
If any dependencies are missing, install them as root.The binary RPMs are built and saved under /rpmbuild/RPMS.
Log in as root and execute this command to install R:
# rpm -i path/rpmbuild/RPMS/R-core_RPM
For example, this command installs R 3.0.1 on Red Hat Enterprise Linux x86-64 version 6, where the path to rpmbuild is /refresh/home/.
# rpm -i /refresh/home/rpmbuild/RPMS/x86_64/R-core-3.0.1-1.el6.x86_64.rpm
Note:
Before installing Oracle R Distribution, verify that your version of Oracle Solaris is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".You can use this command to verify the UNIX version:
% uname -r
To install Oracle R Distribution on Oracle Solaris:
Go to the Oracle Open Source Software Download page for Oracle R Distribution:
Download the files for your installation. The following are the files for R-3.0.1:
For x86 64-bit systems:
ord-3.0.1-sol10-x86-64-sunstudio12u3.tar.gz ord-3.0.1-supporting-sol10-x86-64-sunstudio12u3.tar.gz
For SPARC 64-bit systems:
ord-3.0.1-sol10-sparc-64-sunstudio12u3.tar.gz ord-3.0.1-supporting-sol10-sparc-64-sunstudio12u3.tar.gz
Uncompress the first file, either sol110-x86-64 or sol10-sparc.
Run install.sh as root to install the Solaris PKG file for Oracle R Distribution.
# install.sh
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.
Run the following command to verify that libR.so is picking up its shared library dependencies correctly from the local directory.
# ldd -r /usr/lib/64/R/lib/libR.so
Start R by typing R at the command prompt:
% R
Note:
Before installing Oracle R Distribution, verify that your version of IBM AIX is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".You can use this command to verify the UNIX version:
% uname -r
To install Oracle R Distribution on IBM AIX:
Go to the Oracle Open Source Software Download page for Oracle R Distribution:
Download the files for your installation. The following are the files for R-3.0.1:
ORD.3.0.1.0.bff.gz ord-supporting-aix.tar.gz
Uncompress and untar ord-supporting-aix.tar.gz:
$ gunzip ord-supporting-aix.tar.gz # get ord-supporting-aix.tar $ tar -xvf ord-supporting-aix.tar # extract contents of .tar file $ ls ord-supporting-aix # list of rpms bash-4.2-5.aix5.1.ppc.rpm libpng-devel-1.5.9-1.aix5.1.ppc.rpm cairo-1.10.0-1.aix5.2.ppc.rpm pixman-0.28.2-1.aix5.1.ppc.rpm expat-2.0.1-3.aix5.1.ppc.rpm pkg-config-0.25-2.aix5.1.ppc.rpm fontconfig-2.5.0-1.aix5.1.ppc.rpm readline-6.2-3.aix5.1.ppc.rpm gettext-0.17-1.aix5.1.ppc.rpm readline-devel-6.2-3.aix5.1.ppc.rpm glib2-2.28.6-1.aix5.1.ppc.rpm texinfo-4.13a-2.aix5.1.ppc.rpm info-4.13a-2.aix5.1.ppc.rpm xrender-0.9.1-3.aix5.2.ppc.rpm libiconv-1.14-1.aix5.1.ppc.rpm zlib-1.2.6-1.aix5.1.ppc.rpm libpng-1.5.9-1.aix5.1.ppc.rpm zlib-devel-1.2.6-1.aix5.1.ppc.rpm
You can also download these RPMs from http://www.perzl.org/aix/.
Install the RPMs as root using an rpm command:
$ cd /download_directory
$ su
# rpm -i *.rpm
To upgrade existing dependencies, use:
# rpm -UF *.rpm
If you experience conflicts with dependencies, use:
# rpm -UF --nodeps *.rpm
Add /opt/freeware/lib to the LIBPATH environment variable:
For ksh:
$ export LIBPATH=/opt/freeware/lib:$LIBPATH
For csh:
$ setenv LIBPATH /opt/freeware/lib:$LIBPATH
Ensure that /opt/freeware/lib is before /usr/lib.
Uncompress ORD-2.15.1-aix.bff.gz to get ORD-2.15.1-aix.bff:
$ gunzip ORD.2.15.1.0.bff.gz
To install all the filesets in Oracle R Distribution, execute the installp command (with the apply option) as root:
$ cd /download_directory
$ su
# installp -a -d . ORD # install all the filesets in ORD
You can also install independent filesets:
# installp -a -d . ORD.core # installs only ORE.core # installp -a -d . ORD.devel # installs only ORE.devel
Run ldd to ensure that shared library dependencies were picked up correctly:
$ ldd /usr/lib/R/bin/exec/R $ ldd /usr/lib/R/lib/libR.so (libiconv, libreadline) $ ldd /usr/lib/R/lib/libRlapack.so $ ldd /usr/lib/R/lib/libRblas.so
Add /usr/lib/R/lib to the LIBPATH environment variable:
For ksh:
$ export LIBPATH=/usr/lib/R/lib:$LIBPATH
For csh:
$ setenv LIBPATH /usr/lib/R/lib:$LIBPATH
Before installing Oracle R Distribution, verify that your version of Microsoft Windows is supported by Oracle R Enterprise. Refer to Table 1-1, "Oracle R Enterprise Platform Requirements".
Follow these steps to install Oracle R Distribution on Windows:
Go to the Oracle Open Source Software Download page for Oracle R Distribution:
Under R 3.0.1 Downloads, select Windows 64 bit. Click R Distribution and save the zip file on your computer.
ORE-3.0.1-win.zip
Unzip the file and extract the executable file.
ORE-3.0.1-win.exe
Double click the executable file to start the installation of Oracle R Distribution.
Follow the instructions to complete the installation.
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.
Follow these steps to enable MKL for Oracle R Distribution on a Linux Client:
Install MKL. You can download MKL from the following web site:
http://software.intel.com/en-us/intel-mkl
Note: To install MKL on your computer, you must have an MKL license.
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
Start R and execute the Sys.BlasLapack function:
R> 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).
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
Follow these steps to enable MKL for Oracle R Distribution on a Windows client (64-bit):
Install MKL. You can download MKL from the following web site:
http://software.intel.com/en-us/intel-mkl
Note: To install MKL on your computer, you must have an MKL license.
Add the location of libOrdBlasLoader.dll and mkl_rt.dll to the PATH system environment variable.For instructions, see Section 4.2.2.1, "Creating and Modifying Environment Variables on Windows".
Note:
In a typical installation of Oracle R Distribution 3.0.1,libOrdBlasLoader.dll is located in the R home directory:
C:\Program Files\R\R-3.0.1\bin\x64
In a full installation of MKL 11.1, mkl_rt.dll is located in the Intel MKL Composer XE directory:
C:\Program Files (x86)\Intel\Composer XE 2013 SP
Start R and execute the Sys.BlasLapack function:
R> 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).
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 Section 4.2.2.1:
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