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R Renjin Spark Executor (REX) Library genesis.
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#R Renjin Spark Executor (REX) Library | ||
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||
REX is a Scala library offering access to the scientific computing | ||
power of the R programming language to | ||
[Apache Spark](http://spark.apache.org/) batch and streaming | ||
applications on the JVM. This library is built on top of the | ||
[renjin-r-executor](https://github.com/onetapbeyond/renjin-r-executor) | ||
library, a lightweight solution for integrating R analytics executed on | ||
the [Renjin R interpreter](http://www.renjin.org) into any application | ||
running on the JVM. | ||
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||
> IMPORTANT: | ||
> The Renjin R interpreter for statistical computing is currently a | ||
> work-in-progress and is not yet 100% compatible with GNU R. To find which | ||
> CRAN R packages are currently supported by Renjin you can browse or search | ||
> the [Renjin package repository](http://packages.renjin.org/). As Renjin | ||
> compatibility with GNU R continues to improve, REX is ready to deliver | ||
> those improvements directly to Apache Spark batch and streaming | ||
> applications on the JVM. If Renjin does not meet your needs today then | ||
> I recommend checking out | ||
> [ROSE](https://github.com/onetapbeyond/opencpu-spark-executor), an | ||
> alternative library that today offers access to the full scientific | ||
> computing power of the R programming language to Apache Spark applications. | ||
### REX Motivation | ||
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||
> Where Apache SparkR lets data scientists use Spark from R, REX is | ||
> designed to let Scala and Java developers use R from Spark. | ||
The popular [Apache SparkR](https://github.com/apache/spark/tree/master/R) | ||
package provides a lightweight front-end for data scientists to use | ||
Apache Spark from R. This approach is ideally suited to | ||
investigative analytics, such as ad-hoc and exploratory analysis at scale. | ||
|
||
The REX library attempts to provide the same R analytics capabilities | ||
available to Apache SparkR applications within traditional Spark applications | ||
on the JVM. It does this by exposing new `analyze` operations that execute R | ||
analytics on compatible RDDs. This new facility is designed primarily for | ||
operational analytics and can be used alongside Spark core, SQL, Streaming, | ||
MLib and GraphX. | ||
|
||
If you need to query R machine-learning models, score R prediction models or | ||
leverage any other aspect of the R library within your Spark applications on | ||
the JVM then the REX library may be for you. | ||
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### REX Examples | ||
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A number of example applications are provided to demonstrate the use of the | ||
REX library to deliver R analytics capabilities within any Spark solution. | ||
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- Hello, World! [ [Scala](examples/scala/hello-world) ][ [Java](examples/java/hello-world) ] | ||
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### REX SBT Dependency | ||
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``` | ||
libraryDependencies += "io.onetapbeyond" %% "renjin-spark-executor_2.10" % "1.0" | ||
``` | ||
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### REX Gradle Dependency | ||
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``` | ||
compile 'io.onetapbeyond:renjin-spark-executor_2.10:1.0' | ||
``` | ||
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### REX Spark Package Dependency | ||
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Include the REX package in your Spark application using spark-shell, or spark-submit. | ||
For example: | ||
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``` | ||
$SPARK_HOME/bin/spark-shell --packages io.onetapbeyond:renjin-spark-executor_2.10:1.0 | ||
``` | ||
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### REX Basic Usage | ||
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This library exposes new `analyze` transformations on Spark RDDs of type | ||
`RDD[RenjinTask]`. The following sections demonstrate how to use these new | ||
RDD operations to execute R analytics directly within Spark batch and | ||
streaming applications on the JVM. | ||
|
||
See the [documentation](https://github.com/onetapbeyond/renjin-r-executor) | ||
on the underlying `renjin-r-executor` library for details on building | ||
`RenjinTask` and handling `RenjinResult`. | ||
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### REX Spark Batch Usage | ||
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For this example we assume an input `dataRDD`, then transform it to generate | ||
an RDD of type `RDD[RenjinTask]`. In this example each `RenjinTask` will | ||
execute a block of task specific R code when the RDD is eventually evaluated. | ||
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``` | ||
import io.onetapbeyond.renjin.spark.executor.R._ | ||
import io.onetapbeyond.renjin.r.executor._ | ||
val rTaskRDD = dataRDD.map(data => { | ||
Renjin.R() | ||
.code(rCode) | ||
.input(data.asInput()) | ||
.build() | ||
}) | ||
``` | ||
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The set of `RenjinTask` within `rTaskRDD` can be scheduled for | ||
processing by calling the new `analyze` operation provided by REX | ||
on the RDD: | ||
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``` | ||
val rResultRDD = rTaskRDD.analyze | ||
``` | ||
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When `rTaskRDD.analyze` is evaluated by Spark the resultant `rResultRDD` | ||
is of type `RDD[RenjinResult]`. The result returned by the block of the | ||
task specific R code for the original `RenjinTask` is available | ||
within these `RenjinResult`. These values can be optionally cached, further | ||
processed or persisted per the needs of your Spark application. | ||
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||
Note, the block of task specific R code can make use of any CRAN R | ||
package function or script that is supported by the Renjin R interpreter. | ||
To find which CRAN R packages are currently supported by Renjin you can | ||
browse or search the [Renjin package repository](http://packages.renjin.org/). | ||
|
||
### REX Spark Streaming Usage | ||
|
||
For this example we assume an input stream `dataStream`, then transform | ||
it to generate a new stream with underlying RDDs of type `RDD[RenjinTask]`. | ||
In this example each `RenjinTask` will execute a block of task specific R | ||
code when the stream is eventually evaluated. | ||
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||
``` | ||
import io.onetapbeyond.renjin.spark.executor.R._ | ||
import io.onetapbeyond.renjin.r.executor._ | ||
val rTaskStream = dataStream.transform(rdd => { | ||
rdd.map(data => { | ||
Renjin.R() | ||
.code(rCode) | ||
.input(data.asInput()) | ||
.build() | ||
}) | ||
}) | ||
``` | ||
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The set of `RenjinTask` within `rTaskStream` can be scheduled for processing | ||
by calling the new `analyze` operation provided by REX on each RDD within | ||
the stream: | ||
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``` | ||
val rResultStream = rTaskStream.transform(rdd => rdd.analyze) | ||
``` | ||
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When `rTaskStream.transform` is evaluated by Spark the resultant | ||
`rResultStream` has underlying RDDs of type `RDD[RenjinResult]`. The result | ||
returned by the block of task specific R code for the original | ||
`RenjinTask` is available within these `RenjinResult`. These values can | ||
be optionally cached, further processed or persisted per the needs of your | ||
Spark application. | ||
|
||
Note, the block of task specific R code can make use of any CRAN R | ||
package function or script that is supported by the Renjin R interpreter. | ||
To find which CRAN R packages are currently supported by Renjin you can | ||
browse or search the [Renjin package repository](http://packages.renjin.org/). | ||
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### Traditional v REX Spark Application Deployment | ||
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To understand how REX delivers the scientific computing power of | ||
the R programming language to Spark applications on the JVM the following | ||
sections compare and constrast the deployment of traditional Scala, Java, | ||
Python and SparkR applications with Spark applications powered by the | ||
REX library. | ||
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The sole deployment requirement when working with the REX library is to | ||
add the necessary `Java Archive (.jar)` dependencies to your Spark application | ||
for REX, for the Renjin interpreter itself and for any | ||
[Renjin-compatible CRAN R packages](http://packages.renjin.org/) that | ||
your R code will use. This is discussed in | ||
greater detail in `Application Deployment` section 3. that follows below. | ||
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####1. Traditional Scala | Java | Python Spark Application Deployment | ||
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![Traditional Deployment: Spark](https://onetapbeyond.github.io/resource/img/rex/trad-spark-deploy.jpg) | ||
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Without REX library support, neither data scientists nor application | ||
developers have access to R's analytic capabilities within these types | ||
of application deployments. | ||
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####2. Traditional SparkR Application Deployment | ||
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![Traditional Deployment: SparkR](https://onetapbeyond.github.io/resource/img/rex/trad-sparkr-deploy.jpg) | ||
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While data scientists can leverage the computing power of Spark within R | ||
applications in these types of application deployments, these same R | ||
capabilities are not available to Scala, Java or Python developers. | ||
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Note, when working with Apache SparkR, the R runtime environment must be | ||
installed locally on each worker node on your cluster. | ||
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####3. Scala | Java + R (REX) Spark Application Deployment | ||
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![New Deployment: renjin-spark-executor](https://onetapbeyond.github.io/resource/img/rex/new-rex-deploy.jpg) | ||
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Both data scientists and application developers working in either Scala or | ||
Java can leverage the power of R using the REX library within these | ||
types of application deployments. | ||
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As REX, the Renjin R interpreter and all | ||
[Renjin-compatible CRAN R packages](http://packages.renjin.org/) all | ||
native JVM libraries these dependencies are made available as standard | ||
`JAR` artifacts available for download or inclusion as managed | ||
dependencies from a Maven repository. | ||
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For example, the basic Maven artifact dependency delcarations for a | ||
REX-powered Spark batch application using the `sbt` build tool look | ||
as follows: | ||
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``` | ||
libraryDependencies ++= Seq( | ||
"org.apache.spark" % "spark-core_2.10" % "version" % "provided", | ||
"io.onetapbeyond" % "renjin-spark-executor" % "version", | ||
"org.renjin" % "renjin-script-engine" % "version" | ||
) | ||
``` | ||
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As a further example, the Maven artifact dependencies for a REX-powered | ||
Spark streaming application that depends on the Renjin-compatible CRAN | ||
R `survey` package using the `sbt` build tool look as follows: | ||
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``` | ||
libraryDependencies ++= Seq( | ||
"org.apache.spark" % "spark-streaming_2.10" % "version" % "provided", | ||
"io.onetapbeyond" % "renjin-spark-executor" % "version", | ||
"org.renjin" % "renjin-script-engine" % "version", | ||
"org.renjin.cran" % "survey" % "version" | ||
) | ||
``` | ||
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All Renjin artifacts are maintained within a Maven repository | ||
managed by [BeDataDriven](http://www.bedatadriven.com), the creators | ||
of the Renjin interpreter. To use these artifacts you must identify | ||
the `BeDataDriven` Maven repository to your build tool. For example, | ||
when using `sbt` the required `resolver` is as follows: | ||
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``` | ||
resolvers += | ||
"BeDataDriven" at "https://nexus.bedatadriven.com/content/groups/public" | ||
``` | ||
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Note, as REX is powered by Renjin there is *no need* to install the R | ||
runtime environment locally on each worker node on your cluster. This | ||
means REX works out-of-the box with all new or existing Spark clusters. | ||
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### License | ||
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||
See the [LICENSE](LICENSE) file for license rights and limitations (Apache License 2.0). |
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resolvers += | ||
"BeDataDriven" at "https://nexus.bedatadriven.com/content/groups/public" | ||
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lazy val root = (project in file(".")). | ||
settings( | ||
name := "renjin-spark-executor", | ||
organization := "io.onetapbeyond", | ||
version := "1.0", | ||
scalaVersion := "2.10.6", | ||
libraryDependencies ++= Seq( | ||
"org.apache.spark" % "spark-core_2.10" % "1.6.0" % "provided", | ||
"org.renjin" % "renjin-script-engine" % "0.8.1890" % "provided", | ||
"io.onetapbeyond" % "renjin-r-executor" % "1.2", | ||
"org.scalatest" % "scalatest_2.10" % "2.2.4" % "test" | ||
), | ||
assemblyOption in assembly := (assemblyOption in assembly).value.copy(includeScala = false) | ||
) |
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.gradle | ||
build/ | ||
gradle.properties | ||
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# Ignore Gradle GUI config | ||
gradle-app.setting | ||
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# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored) | ||
!gradle-wrapper.jar | ||
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*.class | ||
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml | ||
hs_err_pid* |
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###Hello, World! | ||
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||
The canonical "Hello, World!" example application that demonstrates | ||
the basic usage of REX to deliver R analytics capabilities within any | ||
Spark solution. | ||
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####Source | ||
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Check out the example source code provided and you'll see that REX | ||
integrates seamlessly within any traditional Spark application. The source | ||
code also provides extensive comments that help guide you through | ||
the integration. | ||
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####Build | ||
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Run the following [Gradle](http://gradle.org/) command within | ||
the `hello-world` directory to build a `fatJar` for the example application | ||
that can then be deployed directly to your Spark cluster. | ||
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`` | ||
gradlew clean shadowJar | ||
`` | ||
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The generated `fatJar` can be found in the `build/libs` directory. | ||
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####Launch | ||
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The simplest way to launch the example application is to use the | ||
[spark-submit](https://spark.apache.org/docs/latest/submitting-applications.html) | ||
shell script provided as part of the Spark distribution. | ||
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The submit command you need should look something like this: | ||
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``` | ||
spark-submit --class io.onetapbeyond.opencpu.spark.executor.examples.HelloWorld --master local[*] /path/to/fat/jar/hello-world-[version]-all.jar | ||
``` |
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buildscript { | ||
repositories { jcenter() } | ||
dependencies { | ||
classpath 'com.github.jengelman.gradle.plugins:shadow:1.2.2' | ||
} | ||
} | ||
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apply plugin: 'java' | ||
apply plugin: 'com.github.johnrengelman.shadow' | ||
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sourceCompatibility = 1.8 | ||
targetCompatibility = 1.8 | ||
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description =""" | ||
Hello, World! | ||
""" | ||
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group = "io.onetapbeyond" | ||
archivesBaseName = "hello-world" | ||
version = "1.0" | ||
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repositories { | ||
jcenter() | ||
mavenCentral() | ||
maven { | ||
url "http://nexus.bedatadriven.com/content/groups/public" | ||
} | ||
} | ||
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dependencies { | ||
compile 'org.apache.spark:spark-core_2.10:1.6.0' | ||
compile 'io.onetapbeyond:renjin-spark-executor_2.10:1.0' | ||
compile 'org.renjin:renjin-script-engine:0.8.1890' | ||
} | ||
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jar { | ||
manifest { | ||
attributes("Implementation-Title": archivesBaseName, | ||
"Implementation-Version": version) | ||
} | ||
} | ||
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shadowJar { | ||
manifest { | ||
attributes 'Main-Class': 'io.onetapbeyond.renjin.spark.executor.examples.HelloWorld' | ||
} | ||
} | ||
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configurations { | ||
// Exclude transitive|provided dependencies from shadowJar | ||
runtime.exclude module: 'spark-core_2.10' | ||
} |
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examples/java/hello-world/gradle/wrapper/gradle-wrapper.properties
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#Wed Dec 09 09:36:38 PET 2015 | ||
distributionBase=GRADLE_USER_HOME | ||
distributionPath=wrapper/dists | ||
zipStoreBase=GRADLE_USER_HOME | ||
zipStorePath=wrapper/dists | ||
distributionUrl=https\://services.gradle.org/distributions/gradle-2.9-bin.zip |
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