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Posted to commits@spark.apache.org by da...@apache.org on 2016/03/28 19:14:34 UTC
spark git commit: [SPARK-12792] [SPARKR] Refactor RRDD to support R
UDF.
Repository: spark
Updated Branches:
refs/heads/master 68c0c460b -> 40984f670
[SPARK-12792] [SPARKR] Refactor RRDD to support R UDF.
Refactor RRDD by separating the common logic interacting with the R worker to a new class RRunner, which can be used to evaluate R UDFs.
Now RRDD relies on RRuner for RDD computation and RRDD could be reomved if we want to remove RDD API in SparkR later.
Author: Sun Rui <ru...@intel.com>
Closes #10947 from sun-rui/SPARK-12792.
Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/40984f67
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/40984f67
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/40984f67
Branch: refs/heads/master
Commit: 40984f67065eeaea731940008e6677c2323dda3e
Parents: 68c0c46
Author: Sun Rui <ru...@intel.com>
Authored: Mon Mar 28 10:14:28 2016 -0700
Committer: Davies Liu <da...@gmail.com>
Committed: Mon Mar 28 10:14:28 2016 -0700
----------------------------------------------------------------------
R/pkg/inst/tests/testthat/test_rdd.R | 8 +
.../scala/org/apache/spark/api/r/RRDD.scala | 328 +----------------
.../scala/org/apache/spark/api/r/RRunner.scala | 367 +++++++++++++++++++
3 files changed, 379 insertions(+), 324 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/spark/blob/40984f67/R/pkg/inst/tests/testthat/test_rdd.R
----------------------------------------------------------------------
diff --git a/R/pkg/inst/tests/testthat/test_rdd.R b/R/pkg/inst/tests/testthat/test_rdd.R
index 3b0c16b..b6c8e1d 100644
--- a/R/pkg/inst/tests/testthat/test_rdd.R
+++ b/R/pkg/inst/tests/testthat/test_rdd.R
@@ -791,3 +791,11 @@ test_that("sampleByKey() on pairwise RDDs", {
expect_equal(lookup(sample, 3)[which.min(lookup(sample, 3))] >= 0, TRUE)
expect_equal(lookup(sample, 3)[which.max(lookup(sample, 3))] <= 2000, TRUE)
})
+
+test_that("Test correct concurrency of RRDD.compute()", {
+ rdd <- parallelize(sc, 1:1000, 100)
+ jrdd <- getJRDD(lapply(rdd, function(x) { x }), "row")
+ zrdd <- callJMethod(jrdd, "zip", jrdd)
+ count <- callJMethod(zrdd, "count")
+ expect_equal(count, 1000)
+})
http://git-wip-us.apache.org/repos/asf/spark/blob/40984f67/core/src/main/scala/org/apache/spark/api/r/RRDD.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/api/r/RRDD.scala b/core/src/main/scala/org/apache/spark/api/r/RRDD.scala
index 588a57e..606ba6e 100644
--- a/core/src/main/scala/org/apache/spark/api/r/RRDD.scala
+++ b/core/src/main/scala/org/apache/spark/api/r/RRDD.scala
@@ -17,21 +17,16 @@
package org.apache.spark.api.r
-import java.io._
-import java.net.{InetAddress, ServerSocket}
-import java.util.{Arrays, Map => JMap}
+import java.util.{Map => JMap}
import scala.collection.JavaConverters._
-import scala.io.Source
import scala.reflect.ClassTag
-import scala.util.Try
import org.apache.spark._
import org.apache.spark.api.java.{JavaPairRDD, JavaRDD, JavaSparkContext}
import org.apache.spark.broadcast.Broadcast
import org.apache.spark.internal.Logging
import org.apache.spark.rdd.RDD
-import org.apache.spark.util.Utils
private abstract class BaseRRDD[T: ClassTag, U: ClassTag](
parent: RDD[T],
@@ -42,188 +37,16 @@ private abstract class BaseRRDD[T: ClassTag, U: ClassTag](
packageNames: Array[Byte],
broadcastVars: Array[Broadcast[Object]])
extends RDD[U](parent) with Logging {
- protected var dataStream: DataInputStream = _
- private var bootTime: Double = _
override def getPartitions: Array[Partition] = parent.partitions
override def compute(partition: Partition, context: TaskContext): Iterator[U] = {
-
- // Timing start
- bootTime = System.currentTimeMillis / 1000.0
+ val runner = new RRunner[U](
+ func, deserializer, serializer, packageNames, broadcastVars, numPartitions)
// The parent may be also an RRDD, so we should launch it first.
val parentIterator = firstParent[T].iterator(partition, context)
- // we expect two connections
- val serverSocket = new ServerSocket(0, 2, InetAddress.getByName("localhost"))
- val listenPort = serverSocket.getLocalPort()
-
- // The stdout/stderr is shared by multiple tasks, because we use one daemon
- // to launch child process as worker.
- val errThread = RRDD.createRWorker(listenPort)
-
- // We use two sockets to separate input and output, then it's easy to manage
- // the lifecycle of them to avoid deadlock.
- // TODO: optimize it to use one socket
-
- // the socket used to send out the input of task
- serverSocket.setSoTimeout(10000)
- val inSocket = serverSocket.accept()
- startStdinThread(inSocket.getOutputStream(), parentIterator, partition.index)
-
- // the socket used to receive the output of task
- val outSocket = serverSocket.accept()
- val inputStream = new BufferedInputStream(outSocket.getInputStream)
- dataStream = new DataInputStream(inputStream)
- serverSocket.close()
-
- try {
-
- return new Iterator[U] {
- def next(): U = {
- val obj = _nextObj
- if (hasNext) {
- _nextObj = read()
- }
- obj
- }
-
- var _nextObj = read()
-
- def hasNext(): Boolean = {
- val hasMore = (_nextObj != null)
- if (!hasMore) {
- dataStream.close()
- }
- hasMore
- }
- }
- } catch {
- case e: Exception =>
- throw new SparkException("R computation failed with\n " + errThread.getLines())
- }
- }
-
- /**
- * Start a thread to write RDD data to the R process.
- */
- private def startStdinThread[T](
- output: OutputStream,
- iter: Iterator[T],
- partition: Int): Unit = {
-
- val env = SparkEnv.get
- val taskContext = TaskContext.get()
- val bufferSize = System.getProperty("spark.buffer.size", "65536").toInt
- val stream = new BufferedOutputStream(output, bufferSize)
-
- new Thread("writer for R") {
- override def run(): Unit = {
- try {
- SparkEnv.set(env)
- TaskContext.setTaskContext(taskContext)
- val dataOut = new DataOutputStream(stream)
- dataOut.writeInt(partition)
-
- SerDe.writeString(dataOut, deserializer)
- SerDe.writeString(dataOut, serializer)
-
- dataOut.writeInt(packageNames.length)
- dataOut.write(packageNames)
-
- dataOut.writeInt(func.length)
- dataOut.write(func)
-
- dataOut.writeInt(broadcastVars.length)
- broadcastVars.foreach { broadcast =>
- // TODO(shivaram): Read a Long in R to avoid this cast
- dataOut.writeInt(broadcast.id.toInt)
- // TODO: Pass a byte array from R to avoid this cast ?
- val broadcastByteArr = broadcast.value.asInstanceOf[Array[Byte]]
- dataOut.writeInt(broadcastByteArr.length)
- dataOut.write(broadcastByteArr)
- }
-
- dataOut.writeInt(numPartitions)
-
- if (!iter.hasNext) {
- dataOut.writeInt(0)
- } else {
- dataOut.writeInt(1)
- }
-
- val printOut = new PrintStream(stream)
-
- def writeElem(elem: Any): Unit = {
- if (deserializer == SerializationFormats.BYTE) {
- val elemArr = elem.asInstanceOf[Array[Byte]]
- dataOut.writeInt(elemArr.length)
- dataOut.write(elemArr)
- } else if (deserializer == SerializationFormats.ROW) {
- dataOut.write(elem.asInstanceOf[Array[Byte]])
- } else if (deserializer == SerializationFormats.STRING) {
- // write string(for StringRRDD)
- // scalastyle:off println
- printOut.println(elem)
- // scalastyle:on println
- }
- }
-
- for (elem <- iter) {
- elem match {
- case (key, value) =>
- writeElem(key)
- writeElem(value)
- case _ =>
- writeElem(elem)
- }
- }
- stream.flush()
- } catch {
- // TODO: We should propogate this error to the task thread
- case e: Exception =>
- logError("R Writer thread got an exception", e)
- } finally {
- Try(output.close())
- }
- }
- }.start()
- }
-
- protected def readData(length: Int): U
-
- protected def read(): U = {
- try {
- val length = dataStream.readInt()
-
- length match {
- case SpecialLengths.TIMING_DATA =>
- // Timing data from R worker
- val boot = dataStream.readDouble - bootTime
- val init = dataStream.readDouble
- val broadcast = dataStream.readDouble
- val input = dataStream.readDouble
- val compute = dataStream.readDouble
- val output = dataStream.readDouble
- logInfo(
- ("Times: boot = %.3f s, init = %.3f s, broadcast = %.3f s, " +
- "read-input = %.3f s, compute = %.3f s, write-output = %.3f s, " +
- "total = %.3f s").format(
- boot,
- init,
- broadcast,
- input,
- compute,
- output,
- boot + init + broadcast + input + compute + output))
- read()
- case length if length >= 0 =>
- readData(length)
- }
- } catch {
- case eof: EOFException =>
- throw new SparkException("R worker exited unexpectedly (cranshed)", eof)
- }
+ runner.compute(parentIterator, partition.index, context)
}
}
@@ -242,19 +65,6 @@ private class PairwiseRRDD[T: ClassTag](
parent, numPartitions, hashFunc, deserializer,
SerializationFormats.BYTE, packageNames,
broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) {
-
- override protected def readData(length: Int): (Int, Array[Byte]) = {
- length match {
- case length if length == 2 =>
- val hashedKey = dataStream.readInt()
- val contentPairsLength = dataStream.readInt()
- val contentPairs = new Array[Byte](contentPairsLength)
- dataStream.readFully(contentPairs)
- (hashedKey, contentPairs)
- case _ => null
- }
- }
-
lazy val asJavaPairRDD : JavaPairRDD[Int, Array[Byte]] = JavaPairRDD.fromRDD(this)
}
@@ -271,17 +81,6 @@ private class RRDD[T: ClassTag](
extends BaseRRDD[T, Array[Byte]](
parent, -1, func, deserializer, serializer, packageNames,
broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) {
-
- override protected def readData(length: Int): Array[Byte] = {
- length match {
- case length if length > 0 =>
- val obj = new Array[Byte](length)
- dataStream.readFully(obj)
- obj
- case _ => null
- }
- }
-
lazy val asJavaRDD : JavaRDD[Array[Byte]] = JavaRDD.fromRDD(this)
}
@@ -297,55 +96,10 @@ private class StringRRDD[T: ClassTag](
extends BaseRRDD[T, String](
parent, -1, func, deserializer, SerializationFormats.STRING, packageNames,
broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) {
-
- override protected def readData(length: Int): String = {
- length match {
- case length if length > 0 =>
- SerDe.readStringBytes(dataStream, length)
- case _ => null
- }
- }
-
lazy val asJavaRDD : JavaRDD[String] = JavaRDD.fromRDD(this)
}
-private object SpecialLengths {
- val TIMING_DATA = -1
-}
-
-private[r] class BufferedStreamThread(
- in: InputStream,
- name: String,
- errBufferSize: Int) extends Thread(name) with Logging {
- val lines = new Array[String](errBufferSize)
- var lineIdx = 0
- override def run() {
- for (line <- Source.fromInputStream(in).getLines) {
- synchronized {
- lines(lineIdx) = line
- lineIdx = (lineIdx + 1) % errBufferSize
- }
- logInfo(line)
- }
- }
-
- def getLines(): String = synchronized {
- (0 until errBufferSize).filter { x =>
- lines((x + lineIdx) % errBufferSize) != null
- }.map { x =>
- lines((x + lineIdx) % errBufferSize)
- }.mkString("\n")
- }
-}
-
private[r] object RRDD {
- // Because forking processes from Java is expensive, we prefer to launch
- // a single R daemon (daemon.R) and tell it to fork new workers for our tasks.
- // This daemon currently only works on UNIX-based systems now, so we should
- // also fall back to launching workers (worker.R) directly.
- private[this] var errThread: BufferedStreamThread = _
- private[this] var daemonChannel: DataOutputStream = _
-
def createSparkContext(
master: String,
appName: String,
@@ -353,7 +107,6 @@ private[r] object RRDD {
jars: Array[String],
sparkEnvirMap: JMap[Object, Object],
sparkExecutorEnvMap: JMap[Object, Object]): JavaSparkContext = {
-
val sparkConf = new SparkConf().setAppName(appName)
.setSparkHome(sparkHome)
@@ -381,83 +134,10 @@ private[r] object RRDD {
}
/**
- * Start a thread to print the process's stderr to ours
- */
- private def startStdoutThread(proc: Process): BufferedStreamThread = {
- val BUFFER_SIZE = 100
- val thread = new BufferedStreamThread(proc.getInputStream, "stdout reader for R", BUFFER_SIZE)
- thread.setDaemon(true)
- thread.start()
- thread
- }
-
- private def createRProcess(port: Int, script: String): BufferedStreamThread = {
- // "spark.sparkr.r.command" is deprecated and replaced by "spark.r.command",
- // but kept here for backward compatibility.
- val sparkConf = SparkEnv.get.conf
- var rCommand = sparkConf.get("spark.sparkr.r.command", "Rscript")
- rCommand = sparkConf.get("spark.r.command", rCommand)
-
- val rOptions = "--vanilla"
- val rLibDir = RUtils.sparkRPackagePath(isDriver = false)
- val rExecScript = rLibDir(0) + "/SparkR/worker/" + script
- val pb = new ProcessBuilder(Arrays.asList(rCommand, rOptions, rExecScript))
- // Unset the R_TESTS environment variable for workers.
- // This is set by R CMD check as startup.Rs
- // (http://svn.r-project.org/R/trunk/src/library/tools/R/testing.R)
- // and confuses worker script which tries to load a non-existent file
- pb.environment().put("R_TESTS", "")
- pb.environment().put("SPARKR_RLIBDIR", rLibDir.mkString(","))
- pb.environment().put("SPARKR_WORKER_PORT", port.toString)
- pb.redirectErrorStream(true) // redirect stderr into stdout
- val proc = pb.start()
- val errThread = startStdoutThread(proc)
- errThread
- }
-
- /**
- * ProcessBuilder used to launch worker R processes.
- */
- def createRWorker(port: Int): BufferedStreamThread = {
- val useDaemon = SparkEnv.get.conf.getBoolean("spark.sparkr.use.daemon", true)
- if (!Utils.isWindows && useDaemon) {
- synchronized {
- if (daemonChannel == null) {
- // we expect one connections
- val serverSocket = new ServerSocket(0, 1, InetAddress.getByName("localhost"))
- val daemonPort = serverSocket.getLocalPort
- errThread = createRProcess(daemonPort, "daemon.R")
- // the socket used to send out the input of task
- serverSocket.setSoTimeout(10000)
- val sock = serverSocket.accept()
- daemonChannel = new DataOutputStream(new BufferedOutputStream(sock.getOutputStream))
- serverSocket.close()
- }
- try {
- daemonChannel.writeInt(port)
- daemonChannel.flush()
- } catch {
- case e: IOException =>
- // daemon process died
- daemonChannel.close()
- daemonChannel = null
- errThread = null
- // fail the current task, retry by scheduler
- throw e
- }
- errThread
- }
- } else {
- createRProcess(port, "worker.R")
- }
- }
-
- /**
* Create an RRDD given a sequence of byte arrays. Used to create RRDD when `parallelize` is
* called from R.
*/
def createRDDFromArray(jsc: JavaSparkContext, arr: Array[Array[Byte]]): JavaRDD[Array[Byte]] = {
JavaRDD.fromRDD(jsc.sc.parallelize(arr, arr.length))
}
-
}
http://git-wip-us.apache.org/repos/asf/spark/blob/40984f67/core/src/main/scala/org/apache/spark/api/r/RRunner.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/api/r/RRunner.scala b/core/src/main/scala/org/apache/spark/api/r/RRunner.scala
new file mode 100644
index 0000000..e8fcada
--- /dev/null
+++ b/core/src/main/scala/org/apache/spark/api/r/RRunner.scala
@@ -0,0 +1,367 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.spark.api.r
+
+import java.io._
+import java.net.{InetAddress, ServerSocket}
+import java.util.Arrays
+
+import scala.io.Source
+import scala.util.Try
+
+import org.apache.spark._
+import org.apache.spark.broadcast.Broadcast
+import org.apache.spark.util.Utils
+
+/**
+ * A helper class to run R UDFs in Spark.
+ */
+private[spark] class RRunner[U](
+ func: Array[Byte],
+ deserializer: String,
+ serializer: String,
+ packageNames: Array[Byte],
+ broadcastVars: Array[Broadcast[Object]],
+ numPartitions: Int = -1)
+ extends Logging {
+ private var bootTime: Double = _
+ private var dataStream: DataInputStream = _
+ val readData = numPartitions match {
+ case -1 =>
+ serializer match {
+ case SerializationFormats.STRING => readStringData _
+ case _ => readByteArrayData _
+ }
+ case _ => readShuffledData _
+ }
+
+ def compute(
+ inputIterator: Iterator[_],
+ partitionIndex: Int,
+ context: TaskContext): Iterator[U] = {
+ // Timing start
+ bootTime = System.currentTimeMillis / 1000.0
+
+ // we expect two connections
+ val serverSocket = new ServerSocket(0, 2, InetAddress.getByName("localhost"))
+ val listenPort = serverSocket.getLocalPort()
+
+ // The stdout/stderr is shared by multiple tasks, because we use one daemon
+ // to launch child process as worker.
+ val errThread = RRunner.createRWorker(listenPort)
+
+ // We use two sockets to separate input and output, then it's easy to manage
+ // the lifecycle of them to avoid deadlock.
+ // TODO: optimize it to use one socket
+
+ // the socket used to send out the input of task
+ serverSocket.setSoTimeout(10000)
+ val inSocket = serverSocket.accept()
+ startStdinThread(inSocket.getOutputStream(), inputIterator, partitionIndex)
+
+ // the socket used to receive the output of task
+ val outSocket = serverSocket.accept()
+ val inputStream = new BufferedInputStream(outSocket.getInputStream)
+ dataStream = new DataInputStream(inputStream)
+ serverSocket.close()
+
+ try {
+ return new Iterator[U] {
+ def next(): U = {
+ val obj = _nextObj
+ if (hasNext) {
+ _nextObj = read()
+ }
+ obj
+ }
+
+ var _nextObj = read()
+
+ def hasNext(): Boolean = {
+ val hasMore = (_nextObj != null)
+ if (!hasMore) {
+ dataStream.close()
+ }
+ hasMore
+ }
+ }
+ } catch {
+ case e: Exception =>
+ throw new SparkException("R computation failed with\n " + errThread.getLines())
+ }
+ }
+
+ /**
+ * Start a thread to write RDD data to the R process.
+ */
+ private def startStdinThread(
+ output: OutputStream,
+ iter: Iterator[_],
+ partitionIndex: Int): Unit = {
+ val env = SparkEnv.get
+ val taskContext = TaskContext.get()
+ val bufferSize = System.getProperty("spark.buffer.size", "65536").toInt
+ val stream = new BufferedOutputStream(output, bufferSize)
+
+ new Thread("writer for R") {
+ override def run(): Unit = {
+ try {
+ SparkEnv.set(env)
+ TaskContext.setTaskContext(taskContext)
+ val dataOut = new DataOutputStream(stream)
+ dataOut.writeInt(partitionIndex)
+
+ SerDe.writeString(dataOut, deserializer)
+ SerDe.writeString(dataOut, serializer)
+
+ dataOut.writeInt(packageNames.length)
+ dataOut.write(packageNames)
+
+ dataOut.writeInt(func.length)
+ dataOut.write(func)
+
+ dataOut.writeInt(broadcastVars.length)
+ broadcastVars.foreach { broadcast =>
+ // TODO(shivaram): Read a Long in R to avoid this cast
+ dataOut.writeInt(broadcast.id.toInt)
+ // TODO: Pass a byte array from R to avoid this cast ?
+ val broadcastByteArr = broadcast.value.asInstanceOf[Array[Byte]]
+ dataOut.writeInt(broadcastByteArr.length)
+ dataOut.write(broadcastByteArr)
+ }
+
+ dataOut.writeInt(numPartitions)
+
+ if (!iter.hasNext) {
+ dataOut.writeInt(0)
+ } else {
+ dataOut.writeInt(1)
+ }
+
+ val printOut = new PrintStream(stream)
+
+ def writeElem(elem: Any): Unit = {
+ if (deserializer == SerializationFormats.BYTE) {
+ val elemArr = elem.asInstanceOf[Array[Byte]]
+ dataOut.writeInt(elemArr.length)
+ dataOut.write(elemArr)
+ } else if (deserializer == SerializationFormats.ROW) {
+ dataOut.write(elem.asInstanceOf[Array[Byte]])
+ } else if (deserializer == SerializationFormats.STRING) {
+ // write string(for StringRRDD)
+ // scalastyle:off println
+ printOut.println(elem)
+ // scalastyle:on println
+ }
+ }
+
+ for (elem <- iter) {
+ elem match {
+ case (key, value) =>
+ writeElem(key)
+ writeElem(value)
+ case _ =>
+ writeElem(elem)
+ }
+ }
+ stream.flush()
+ } catch {
+ // TODO: We should propogate this error to the task thread
+ case e: Exception =>
+ logError("R Writer thread got an exception", e)
+ } finally {
+ Try(output.close())
+ }
+ }
+ }.start()
+ }
+
+ private def read(): U = {
+ try {
+ val length = dataStream.readInt()
+
+ length match {
+ case SpecialLengths.TIMING_DATA =>
+ // Timing data from R worker
+ val boot = dataStream.readDouble - bootTime
+ val init = dataStream.readDouble
+ val broadcast = dataStream.readDouble
+ val input = dataStream.readDouble
+ val compute = dataStream.readDouble
+ val output = dataStream.readDouble
+ logInfo(
+ ("Times: boot = %.3f s, init = %.3f s, broadcast = %.3f s, " +
+ "read-input = %.3f s, compute = %.3f s, write-output = %.3f s, " +
+ "total = %.3f s").format(
+ boot,
+ init,
+ broadcast,
+ input,
+ compute,
+ output,
+ boot + init + broadcast + input + compute + output))
+ read()
+ case length if length >= 0 =>
+ readData(length).asInstanceOf[U]
+ }
+ } catch {
+ case eof: EOFException =>
+ throw new SparkException("R worker exited unexpectedly (cranshed)", eof)
+ }
+ }
+
+ private def readShuffledData(length: Int): (Int, Array[Byte]) = {
+ length match {
+ case length if length == 2 =>
+ val hashedKey = dataStream.readInt()
+ val contentPairsLength = dataStream.readInt()
+ val contentPairs = new Array[Byte](contentPairsLength)
+ dataStream.readFully(contentPairs)
+ (hashedKey, contentPairs)
+ case _ => null
+ }
+ }
+
+ private def readByteArrayData(length: Int): Array[Byte] = {
+ length match {
+ case length if length > 0 =>
+ val obj = new Array[Byte](length)
+ dataStream.readFully(obj)
+ obj
+ case _ => null
+ }
+ }
+
+ private def readStringData(length: Int): String = {
+ length match {
+ case length if length > 0 =>
+ SerDe.readStringBytes(dataStream, length)
+ case _ => null
+ }
+ }
+}
+
+private object SpecialLengths {
+ val TIMING_DATA = -1
+}
+
+private[r] class BufferedStreamThread(
+ in: InputStream,
+ name: String,
+ errBufferSize: Int) extends Thread(name) with Logging {
+ val lines = new Array[String](errBufferSize)
+ var lineIdx = 0
+ override def run() {
+ for (line <- Source.fromInputStream(in).getLines) {
+ synchronized {
+ lines(lineIdx) = line
+ lineIdx = (lineIdx + 1) % errBufferSize
+ }
+ logInfo(line)
+ }
+ }
+
+ def getLines(): String = synchronized {
+ (0 until errBufferSize).filter { x =>
+ lines((x + lineIdx) % errBufferSize) != null
+ }.map { x =>
+ lines((x + lineIdx) % errBufferSize)
+ }.mkString("\n")
+ }
+}
+
+private[r] object RRunner {
+ // Because forking processes from Java is expensive, we prefer to launch
+ // a single R daemon (daemon.R) and tell it to fork new workers for our tasks.
+ // This daemon currently only works on UNIX-based systems now, so we should
+ // also fall back to launching workers (worker.R) directly.
+ private[this] var errThread: BufferedStreamThread = _
+ private[this] var daemonChannel: DataOutputStream = _
+
+ /**
+ * Start a thread to print the process's stderr to ours
+ */
+ private def startStdoutThread(proc: Process): BufferedStreamThread = {
+ val BUFFER_SIZE = 100
+ val thread = new BufferedStreamThread(proc.getInputStream, "stdout reader for R", BUFFER_SIZE)
+ thread.setDaemon(true)
+ thread.start()
+ thread
+ }
+
+ private def createRProcess(port: Int, script: String): BufferedStreamThread = {
+ // "spark.sparkr.r.command" is deprecated and replaced by "spark.r.command",
+ // but kept here for backward compatibility.
+ val sparkConf = SparkEnv.get.conf
+ var rCommand = sparkConf.get("spark.sparkr.r.command", "Rscript")
+ rCommand = sparkConf.get("spark.r.command", rCommand)
+
+ val rOptions = "--vanilla"
+ val rLibDir = RUtils.sparkRPackagePath(isDriver = false)
+ val rExecScript = rLibDir(0) + "/SparkR/worker/" + script
+ val pb = new ProcessBuilder(Arrays.asList(rCommand, rOptions, rExecScript))
+ // Unset the R_TESTS environment variable for workers.
+ // This is set by R CMD check as startup.Rs
+ // (http://svn.r-project.org/R/trunk/src/library/tools/R/testing.R)
+ // and confuses worker script which tries to load a non-existent file
+ pb.environment().put("R_TESTS", "")
+ pb.environment().put("SPARKR_RLIBDIR", rLibDir.mkString(","))
+ pb.environment().put("SPARKR_WORKER_PORT", port.toString)
+ pb.redirectErrorStream(true) // redirect stderr into stdout
+ val proc = pb.start()
+ val errThread = startStdoutThread(proc)
+ errThread
+ }
+
+ /**
+ * ProcessBuilder used to launch worker R processes.
+ */
+ def createRWorker(port: Int): BufferedStreamThread = {
+ val useDaemon = SparkEnv.get.conf.getBoolean("spark.sparkr.use.daemon", true)
+ if (!Utils.isWindows && useDaemon) {
+ synchronized {
+ if (daemonChannel == null) {
+ // we expect one connections
+ val serverSocket = new ServerSocket(0, 1, InetAddress.getByName("localhost"))
+ val daemonPort = serverSocket.getLocalPort
+ errThread = createRProcess(daemonPort, "daemon.R")
+ // the socket used to send out the input of task
+ serverSocket.setSoTimeout(10000)
+ val sock = serverSocket.accept()
+ daemonChannel = new DataOutputStream(new BufferedOutputStream(sock.getOutputStream))
+ serverSocket.close()
+ }
+ try {
+ daemonChannel.writeInt(port)
+ daemonChannel.flush()
+ } catch {
+ case e: IOException =>
+ // daemon process died
+ daemonChannel.close()
+ daemonChannel = null
+ errThread = null
+ // fail the current task, retry by scheduler
+ throw e
+ }
+ errThread
+ }
+ } else {
+ createRProcess(port, "worker.R")
+ }
+ }
+}
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