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©2011 Oracle – All Rights Reserved
Oracle R Enterprise – Training Sessions
Session 1: Getting Started with Oracle R Enterprise
Mark Hornick, Senior Manager, Development
Oracle Advanced Analytics
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The following is intended to outline our general product direction.
It is intended for information purposes only, and may not be
incorporated into any contract. It is not a commitment to deliver
any material, code, or functionality, and should not be relied upon
in making purchasing decisions.
The development, release, and timing of any features or
functionality described for Oracle’s products remain at the sole
discretion of Oracle.
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Oracle R Enterprise Training Sessions
Date / Time Session Topics
Thursday, December 1, 2:00 PM ET Getting Started with Oracle R Enterprise
(ORE)
Oracle R Enterprise Overview
Installation of R
Installation of Oracle R Enterprise
Connecting to Exadata from R
Tuesday, December 6, 11:00 AM ET Introduction to the R Language and
Environment
R Language Basics
Producing Graphs in R
Thursday, December 8, 2:00 PM ET ORE Transparency Layer Interacting with Database Tables
Manipulating and transforming data through ORE
Tuesday, December 13, 11:00 AM ET ORE Embedded R Script Execution Execution through R interface
Execution through SQL interface
Thursday, December 15, 2:00 PM ET Operationalizing R Scripts From Analyst to Production
Integration with OBIEE
XML graph generation using SQL
Tuesday, December 20, 11:00 AM ET Advanced Topics Base SAS equivalent functionality
ORE support for Hadoop and Map-Reduce
Use of ORE in Exadata and BDA environments
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Getting Started with Oracle R Enterprise (ORE)
• Oracle R Enterprise Overview
• Installing R
• Installing Oracle R Enterprise
• Connecting to Exadata from R
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Oracle R Enterprise Overview
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What is R?
• R is an Open Source language and environment for
statistical computing and graphics
http://www.r-project.org/
• Started in 1994 as an Alternative to SAS, SPSS & Other
proprietary Statistical Environments
• The R environment – R is an integrated suite of software facilities for data manipulation,
calculation and graphical display
• Around 2 million R users worldwide – Widely taught in Universities
– Many Corporate Analysts know and use R
• Hundreds of open sources packages to enhance
productivity such as: – Bioinformatics with R
– Spatial Statistics with R
– Financial Market Analysis with R
– Linear and Non Linear Modeling
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Why statisticians/data analysts use R
R environment is…
• Powerful
• Extensible
• Graphical
• Extensive statistics
• OOTB functionality with
many ‘knobs’ but
smart defaults
• Ease of installation and use
• Free
Statisticians typically are…
• Not SQL literate
• Not familiar with DBA tasks
R is a statistics language similar to Base SAS or SPSS statistics
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Limitations of R
• R is a client and server bundled together as 1 executable - like Excel
– Single user tool
– Not multi-threaded
– Cannot leverage CPU capacity even on a user's laptop/desktop
• R requires data it operates on to be first loaded into memory
– Loading data may not be a limitation given RAM available on laptops/desktops
– R’s call by value semantics means as data flows into functions, for each function
invocation, many copies of the data are made
– As a result you quickly run into memory limits
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Why should you be interested in R?
• Emerging trends
– It’s the next “big thing” in advanced analytics
– Colleges and universities use R for statistics classes (replacing more traditional software tools)
– Advanced Analytics as a critical differentiator of the DWH technology stack
• Augment Oracle deployments
– Enhance results with powerful graphics
– Integrate R results and graphics with BI Publisher documents and OBIEE
dashboards
• A scalable R via Oracle R Enterprise
– Leverage Oracle-engineered solutions
– A worthy alternative to SAS
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Rexer Analytics Survey 2011
http://www.rexeranalytics.com/Data-Miner-Survey-Results-2010.html ©2011 Oracle – All Rights Reserved
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R Ecosystem Resources
• Many helpful books
– http://www.r-project.org/doc/bib/R-publications.html
• Installation and Administration
– http://cran.r-project.org/doc/manuals/R-admin.html
• User Groups
• UseR Conferences
• Huge libraries of reusable code
– Visit CRAN: http://cran.r-project.org/
• Well-documented packages
– With sample data and code
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Default R GUI
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RStudio – Third Party, Open Source IDE
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http://www.kdnuggets.com/polls/2011/r-gui-used.html
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Data Visualization with R
http://addictedtor.free.fr/graphiques/
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Graph examples…
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Oracle Strategy for R
Deliver enterprise-level advanced analytics based on R environment
1. Oracle’s Distribution of Open Source R
• Enterprise support for open-source R
• Enhanced performance with Intel MKL libraries for x86 hardware
• Packaged with Oracle Linux distribution
2. Oracle R Enterprise
• Embedded component of the RDBMS
• Eliminates R’s memory constraint by enabling R to work transparently on database resident data
• Brings R users closer to Oracle Database by transparently leveraging in-database analytics via R
• Enables R users to leverage Oracle Database and Big Data Appliance for scalable R Analytics
• Enables integration of R scripts into enterprise production applications and OBIEE dashboards
• Fully leverages the latest R algorithms and models contributed
to the Comprehensive R Archive Network (CRAN)
• Integrated with Hadoop and HDFS – write map-reduce style R scripts
• Enables migration away from Base SAS and helps reduce SA$ Annual Usage Fees
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Oracle R Distribution
• Features
– Supported by Oracle
– Optimized for high performance analytics using Intel MKL Library
• Platforms
– Windows 32-bit, 64-bit
– Linux 64-bit
• Integrated with
Oracle Enterprise Linux distribution
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R Licensing and Distribution
• Open source R is licensed under GPL-v2
– http://www.gnu.org/licenses/gpl-2.0.html
• Oracle will redistribute open source R providing free support
for Oracle Database and Oracle Linux customers
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Oracle R Enterprise
Function push-down – data transformation & statistics
R workspace console
Oracle statistics engine
OBIEE, Web Services
No changes to the user
experience
Scale to large data sets
Embed in operational
systems
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Oracle R Enterprise
Transparently leverage Hadoop for High Performance Analytics to Big Data Appliance
Function push-down – data transformation & statistics
R workspace console
Oracle statistics engine
OBIEE, Web Services
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Big Data Appliance
• An engineered system optimized for capturing
and integrating “low density” data into Exadata
• High-performance Hardware • Optimized for Hadoop and NoSQL workloads
• InfiniBand Networking for integration with Exadata
• Software: • Oracle Hadoop
• Oracle R Enterprise
• Oracle NoSQL DB
• Oracle Data Integrator (Hadoop capabilities)
• Oracle Loader for Hadoop
18 Sun X4270 M2 Servers
48 GB memory per node = 864 GB memory
12 Intel cores per node = 216 cores
24 TB storage per node = 432 TB storage
40 Gb p/sec InfiniBand
10 Gb p/sec Ethernet
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BDA and Exadata
HDFS Hadoop
ORE ORHC
Load Data to Exadata
Analyze Data
Exadata
BDA
Oracle Database
ORE
R Engine
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What R programmers should know…
Oracle R Enterprise…
• provides a familiar environment to operate on data in Oracle Database
• overloads base R functions for data in Oracle Database to address big
data as a single big data set problem
• enables embedded execution of existing R scripts in Oracle Database to
address big data
• enables embedding advanced analytics into production infrastructure
and business processes / applications
• provides database-controlled data-parallel execution framework
• removes need to manage data outside the database
• no knowledge of SQL required
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What statisticians should know…
Oracle R Enterprise…
• expands the kinds of problems that can be solved using readily available
technologies through in-database statistical calculations
• Reduces the SQL skills required to get results
• reduces time programmers spend on building infrastructure to manage
data outside of Oracle Database
• reduces the complexity of analytic solutions to be placed into production
• reduces costs by replacing SAS, and its high licensing fees, in the lab
• provides exhaustive support for statistical techniques and functions
found in Base SAS and Base R
• implements select techniques from SAS libraries: STAT, ETS and OR
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What a SQL user or DBA should know …
Oracle R Enterprise…
• is an advanced analytical engine that can be used in addition to SQL in
Oracle Database
• can be used to put an R script into production through SQL invocation
• reduces or eliminates the need to move data outside Oracle Database
• facilitates auditing of data flows
• reduces the number of LOB help requests for SQL queries to obtain
data of interest
• enables embracing high impact advanced analytic workloads to run
within production database infrastructure
• allows DBAs to control what R code runs within a deployment by
requiring all R code reside in a secure, audited database table
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What is Oracle R Enterprise?
• R packages, database library, and SQL extensions that bring Oracle Database closer to Advanced Analytics
users in an Enterprise
– Transparency Layer
• Set of packages mapping R data types to Oracle Database objects
• Transparent SQL generation for R expressions on mapped data types
• Enables direct interaction with database-resident data using R language constructs
• Enables R users to work with data larger than desktop system memory
– Statistics Engine
• Set of statistical functions and procedures for commonly-used statistical libraries
• Executes in Oracle Database
– SQL extensions
• Enables database server execution of R code to facilitate embedding R in operational systems
• Eliminates client data loading and result write-back to Oracle Database
• Enables dataflow parallelism, generation of rich XML output, SQL access to R, and parallel simulations capability
– Hadoop Connector
• R packages that enable working directly with an Oracle Hadoop cluster using R
• Data resides in HDFS, Oracle Database ,or local files
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Oracle R Enterprise Compute Engines
• R-SQL Transparency Layer intercepts R
functions for scalable in-db execution
• Function intercept for data transforms,
statistical functions and advanced analytics
• Interactive display of graphical results and
flow control as in standard R
• Submit entire R scripts for embedded
execution by Oracle Database
• Connect to Oracle Hadoop Cluster and
interact with HDFS data
• Scale to large datasets
• Access tables, views, and external
tables, as well as data through
DB LINKS
• Leverage database SQL parallelism
• Leverage new and existing
in-database statistical and data mining
capabilities
R Engine Other R packages
Oracle R Enterprise packages
User R Engine on desktop
• Database can spawn multiple R
engines for database-managed
parallelism
• Efficient data transfer to spawned
R engines
• Emulate map-reduce style algorithms
and applications
• Enables “lights-out” execution of R
scripts
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User tables
Oracle Database SQL
Results
Database Compute Engine
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R Engine Other R packages
Oracle R Enterprise packages
R Engine(s) spawned by Oracle DB
R
Results
3
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Oracle R Enterprise – Data Sources
User tables
Oracle Database
Bulk import
File systems Other databases
Database Links
SQL Results
R Engine Other R packages
Oracle R package
R user on desktop
External Tables
File systems
Direct R access
Other databases
Direct R access
RODBC, DBI, etc
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OLAP
cubes
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Installing R
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Installing R
• Go to http://cran.r-project.org/ and choose
Linux, Mac or Windows
• If Windows
– Click “install R for the first time”
– Click “previous releases”
– Click “Download R 2.13.2 for Windows”
• If Linux
– Click “R Sources” under software
– Click “R-2.13.2.tar.gz” to download
– Build R on your Linux system
• If Mac
– …note ORE not supported on Mac
• Repeat the same process to install R on Oracle Database node(s)
• For more info than you’d want, see http://cran.r-project.org/doc/manuals/R-admin.html
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Other R GUIs, e.g., installing RStudio
• Go to http://rstudio.org/
• Click
• Click for desktop
• Consider server install if you run R on a Linux server and
want to enable users to remotely
access RStudio using a web browser
• Installation instructions online
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Running R on Windows
• Double click the desktop icon
• Run from C:\Program Files\R\R-2.13.2\bin\x64\Rgui.exe
• At the command prompt ‘R>’
– help.start() brings up help in your default browser
– plot(mtcars) get a quick pairs plot of the variables in mtcars
• Quit R
– quit()
– Or use: File Exit
– Save workspace image?
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Installing R on Linux
• Download R-2.13.2 source tar file from CRAN
– http://cran.r-project.org/
• Untar the file
– tar -zxvf R-2.13.2.tar.gz
• Change directory to R-2.13.2
– cd R-2.13.2
• Configure for shared library generation
– ./configure --with-ICU=no --enable-R-shlib
– make
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Setting Environment Variables on Linux
• Set R_HOME environment variable to R root installation
– If RPM-based install using Oracle R Distribution setenv R_HOME /usr/lib64/R
– If manual R installation setenv R_HOME <dir-where-ran-make>
• Set PATH environment variable
– Add $R_HOME/bin to PATH
– If RPM-based instlal using Oracle R Distribution
setenv PATH /usr/bin:$PATH
– If manual R installation
setenv PATH <dir-where-ran-make>/bin:$PATH
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Running R on Linux
• Run R
– $R_HOME/bin/R, or just R
– For the GUI, R --gui=Tk
• At the command prompt ‘R>’
– help.start() brings up help in your default browser
– plot(mtcars) get a quick pairs plot of the variables in mtcars
• Quit R
– quit()
– Or use: Cntrl-D Cntrl-D
– Save workspace image?
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Installing Oracle R Enterprise
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Supported Configurations
• Oracle Database 11.2 series on Oracle Linux 5, 64 bit
– Exadata machines
– Oracle Database
• Oracle R Enterprise client
– Windows XP/Vista/7 32 bit or 64 bit
– Oracle Enterprise Linux 64 bit
• Hadoop Connector only deployed on Oracle Hadoop cluster
• See ORE Beta Release Notes
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ORE Installation steps
• Install Oracle Database 11.2 series
• Install R
– ORE certified with R-2.13.2
• Install ORE
• Set up Rprofile
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Prerequisites for ORE
• Oracle Database 11.2 series
– Version 11.2.0.3, or
– If using 11.2.0.1 or 11.2.0.2, must include patch that fixes Bug Number 11678127
• R installed on…
– user’s desktop to connect to and work with Oracle Database
– Oracle Database node(s) used as database-embedded R engine
• Two R package must be installed
– Download DBI: http://cran.r-project.org/web/packages/DBI/index.html or R> install.packages(“DBI”)
– Download PNG: http://cran.r-project.org/web/packages/png/index.html or R> install.packages(“png”)
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Database Patches
• Download the 11.2.0.3 patch set for Enterprise Edition
from My Oracle Support
OR
• Linux 64-bit
– For Oracle 11.2.0.1.0: Patch number 12598677 for Linux x86-64
– For Oracle 11.2.0.2.0: Patch number 12976544 for Linux x86-64
• Windows XP 32-bit
– For Oracle 11.2.0.2 Patch 11 fixes Bug Number 11678127
• Windows 7 32-bit and 64-bit
– For Oracle 11.2.0.2 Patch 11 fixes Bug Number 11678127
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Applying the Database Patch for Linux
• Install the patch to Oracle Database, if needed
cd DBpatch
setenv PATH $ORACLE_HOME/OPatch:$PATH
unzip -d . p11678127_112010_Linux-x86-64.zip
cd 11678127
opatch apply
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Installing the ORE Package
• From R command line for both ORE client and database server
– Choose URL appropriate for platform
R
R> remove.packages(c("ORExml", "ORExml", "OREeda",
"OREgraphics", "OREstats", "OREbase", "ORE", "ROracle"))
R> install.packages("ORE", repos =
"http://adc2100203.us.oracle.com:8080/CRAN")
• Check package installation by invoking… R> library(ROracle)
Note: installing ORE package on database server is only
required if planning to use embedded R execution
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Installing Oracle Instant Client on Linux
• Obtain the RPM files – oracle-instantclient11.2-basic-11.2.0.3.0-1.x86_64.rpm
– oracle-instantclient11.2-devel-11.2.0.3.0-1.x86_64.rpm
– http://www.oracle.com/technetwork/database/features/instant-client/index-097480.html
• Install the RPMs sudo rpm –ivh oracle-instantclient11.2-basic-11.2.0.3.0-1.x86_64.rpm
sudo rpm –ivh oracle-instantclient11.2-devel-11.2.0.3.0-1.x86_64.rpm
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Installing ORE Server Components on Windows
• Download ORE server components from location specified when you
enrolled in the Beta test
– Internal: https://stbeehive.oracle.com/teamcollab/overview/Oracle+R+Enterprise+Beta+Software+Download
rqe_install_win.zip
• Unzip the download into an empty directory, e.g., C:\rqe_install_win
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Set Windows Environment Variables
for ORE server
• Set R_HOME to the directory where R is installed
– for example, C:\Program Files\R\R-2.13.2, if you installed R in the default location
• Set R_PROFILE_USER to the location where the Rprofile is stored
– Default value is C:\Program Files\R\Rprofile
– This can be changed
• Bounce the database
– As sysdba in SQL*Plus execute…
shutdown immediate
startup
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Running the Windows install script for ORE server
• In a Command Window, change directory to where downloaded file unzipped
• Change directory to the server folder
• Run install.bat
• Change directory to data folder
• Run install.bat
• The installation scripts automatically create…
– User account rquser (password rquser) in your database
Note: If an account named rquser already exists, rename the account
– Demo tables in the database
– Rprofile file which tells R to connect to a specific database when starting R
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Location of Windows Installed Files
• Client-side packages in $R_HOME/library
– Database Connectivity packages: DBI, ROracle
– ORE Client: ORE, OREbase, OREeda, OREgraphics, OREstats, ORExml
– ORE Hadoop client: ORHC
• Server-side (database)
– ORE libraries in $ORACLE_HOME/bin
– ore.dll and rqe.dll
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Start R on Windows with ORE
• Click desktop icon, or
• Click, e.g., C:\Program Files\R\R-2.13.1\bin\i386\Rgui.exe
• Type ore.ls() to see
a list of available tables
Confirms database connectivity
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.Rprofile
options(prompt='ORE> ')
options(width=132)
.First <- function()
{
# Load Oracle R libraries.
library(ORE)
# Database credentials:
user = “my_schema“
password = “my_password“
sid = “MY_ORACLE_SID"
host = “MY_DB_HOST"
cat("Connecting to ORE\n")
cat(" User:", user, "\n")
cat(" SID: ", sid, "\n")
cat(" Host:", host, "\n")
ore.connect(user, sid, host, password)
ore.sync()
ore.attach()
cat("Connected.\n")
}
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Installing ORE Server Components on Linux
• Download ORE from the location specified when you
enrolled in the Beta test
• Unzip the download into an empty directory, e.g.,
~/OREbeta
• Install database server-side components
– Log in as user oracle
cd server
./install.sh
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Location of Linux Installed Files
• Client-side packages in in $R_HOME/library
– Database Connectivity packages: DBI, ROracle
– ORE Client: ORE, OREbase, OREeda, OREgraphics, OREstats, ORExml
– ORE Hadoop client: ORHC
• Server-side (database)
– ORE libraries in $ORACLE_HOME/lib
– ore.so and librqe.so
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Enable and Check Database Connectivity
• Enable database connectivity on R startup
– Copy provided Rprofile file to the home directory
cp Rprofile ~/.Rprofile
– Set R_PROFILE USER environment variable
setenv R_PROFILE_USER ~/.Rprofile
• Bounce the database, as sysdba execute
shutdown immediate
startup
• Check database connectivity
– Start R
– Execute ore.ls()
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Sample Code
• ORE shipped with examples illustrating how to use ORE
– A collection of self-contained R scripts
• Scripts located in <unzip-directory>/samples.tar
– Where <unzip-directory> is the directory where you
unzipped the ORE download
– Unzip samples.tar
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Troubleshooting
• See log.txt file
– created in directory where you executed install program
– View file to review errors
• Install program can be re-executed after correcting errors
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Uninstalling ORE
Client Components
• Start R and invoke
remove.packages(“OREeda”)
remove.packages(“OREgraphics”)
remove.packages(“OREstats”)
remove.packages(“OREbase”)
remove.packages(“ORExml”)
remove.packages(“ORE”)
remove.packages(“ROracle”)
remove.packages(“DBI”)
• Unset environment variable unsetenv R_PROFILE_USER
Database Server Components
• As sysdba, execute in SQL*Plus
SQL> drop user rqsys cascade;
• On linux command line, execute
rm $ORACLE_HOME/bin/ore.so
rm $ORACLE_HOME/bin/librqe.so
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Connecting to Exadata (Oracle Database) from R
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Connecting to Exadata (Oracle Database) from R
• You’ve already done it
by starting R with Rprofile
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Oracle R Enterprise Initial connection and basic operations
R> ore.connect("rquser", "orcl", "machine-1")
R> ore.sync("rquser")
R> ore.attach ("rquser")
R> ore.ls()
R> names(ONTIME_S)
R> dim(ONTIME_S)
Implicitly invoked through R_PROFILE_USER
Sync database objects with R client, e.g., add/remove tables/views added via SQL*Plus)
List tables visible in schema rquser as ore.frame objects
List columns associated with table ONTIME_S
View the number of rows and columns associated with this ore.frame
Add schema objects in R env search path
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Working with ORE Connections
ore.connect("RQUSER","SID","HOST","PASSWORD",1521)
ore.create( ONTIME_S, table = "NEW_ONTIME_S")
ore.create( ONTIME_S, view = "NEW_ONTIME_S_VIEW")
ore.drop(table="NEW_ONTIME_S")
ore.drop(view="NEW_ONTIME_S_VIEW")
v <- ore.push(c(1,2,3,4,5))
ore.sync()
ore.sync("RQUSER")
ore.sync(table=c("ONTIME_S", "NARROW"))
ore.sync("RQUSER", table=c("ONTIME_S", "NARROW"))
ore.exists("ONTIME_S", "RQUSER")
Connect to a specific schema and database
One connection active at a time
Create a database table from a data.frame, ore.frame. Create a view from an ore.frame.
Drop table or view in database
Store R object in database as temporary object, returns handle to object. Data frame, matrix, and vector to table, list/model/others to serialized object
Synchronize ORE proxy objects in R with tables/views available in database, on a per schema basis
Returns TRUE if named table or view exists in schema
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Working with ORE Connections ore.ls()
ore.ls("RQUSER")
ore.ls("RQUSER",all.names=TRUE)
ore.ls("RQUSER",all.names=TRUE, pattern= "NAR")
t <- ore.get("ONTIME_S","RQUSER")
ore.attach("RQUSER")
ore.attach("RQUSER", pos=2)
ore.detach("RQUSER")
ore.rm("DF1")
ore.rm(list("TABLE1","TABLE2"), "RQUSER")
ore.disconnect()
ore.exec("create table F2 as select * from ONTIME_S")
List the objects available in ORE environment mapped to database schema.
All.names=FALSE excludes names starting with a ‘.’
Obtain object to named table/view in schema.
Make database objects visible in R for named schema. Can place corresponding environment in specific position in env path.
Remove schema’s environment from the object search path.
Remove table or view from schema’s R environment.
Disconnect from the database. Clean up all associated R objects and temporary database schema objects
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Execute SQL or PL/SQL without return value
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Demonstration
• Connecting to ORE
• Manipulating database objects
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Wrapping up…
• What’s Oracle R Enterprise
• Install R and ORE
• Interacting with Oracle Database through R
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