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author | cafreeman <cfreeman@alteryx.com> | 2015-04-17 13:42:19 -0700 |
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committer | Shivaram Venkataraman <shivaram@cs.berkeley.edu> | 2015-04-17 13:42:19 -0700 |
commit | 59e206deb7346148412bbf5ba4ab626718fadf18 (patch) | |
tree | cf4435a81197e76957c4afdcc48686a6e46dc5dc /core/src | |
parent | a83571acc938582865efb41645aa1e414f339e46 (diff) | |
download | spark-59e206deb7346148412bbf5ba4ab626718fadf18.tar.gz spark-59e206deb7346148412bbf5ba4ab626718fadf18.tar.bz2 spark-59e206deb7346148412bbf5ba4ab626718fadf18.zip |
[SPARK-6807] [SparkR] Merge recent SparkR-pkg changes
This PR pulls in recent changes in SparkR-pkg, including
cartesian, intersection, sampleByKey, subtract, subtractByKey, except, and some API for StructType and StructField.
Author: cafreeman <cfreeman@alteryx.com>
Author: Davies Liu <davies@databricks.com>
Author: Zongheng Yang <zongheng.y@gmail.com>
Author: Shivaram Venkataraman <shivaram.venkataraman@gmail.com>
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Author: Sun Rui <rui.sun@intel.com>
Closes #5436 from davies/R3 and squashes the following commits:
c2b09be [Davies Liu] SQLTypes -> schema
a5a02f2 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R3
168b7fe [Davies Liu] sort generics
b1fe460 [Davies Liu] fix conflict in README.md
e74c04e [Davies Liu] fix schema.R
4f5ac09 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R5
41f8184 [Davies Liu] rm man
ae78312 [Davies Liu] Merge pull request #237 from sun-rui/SPARKR-154_3
1bdcb63 [Zongheng Yang] Updates to README.md.
5a553e7 [cafreeman] Use object attribute instead of argument
71372d9 [cafreeman] Update docs and examples
8526d2e71 [cafreeman] Remove `tojson` functions
6ef5f2d [cafreeman] Fix spacing
7741d66 [cafreeman] Rename the SQL DataType function
141efd8 [Shivaram Venkataraman] Merge pull request #245 from hqzizania/upstream
9387402 [Davies Liu] fix style
40199eb [Shivaram Venkataraman] Move except into sorted position
07d0dbc [Sun Rui] [SPARKR-244] Fix test failure after integration of subtract() and subtractByKey() for RDD.
7e8caa3 [Shivaram Venkataraman] Merge pull request #246 from hlin09/fixCombineByKey
ed66c81 [cafreeman] Update `subtract` to work with `generics.R`
f3ba785 [cafreeman] Fixed duplicate export
275deb4 [cafreeman] Update `NAMESPACE` and tests
1a3b63d [cafreeman] new version of `CreateDF`
836c4bf [cafreeman] Update `createDataFrame` and `toDF`
be5d5c1 [cafreeman] refactor schema functions
40338a4 [Zongheng Yang] Merge pull request #244 from sun-rui/SPARKR-154_5
20b97a6 [Zongheng Yang] Merge pull request #234 from hqzizania/assist
ba54e34 [Shivaram Venkataraman] Merge pull request #238 from sun-rui/SPARKR-154_4
c9497a3 [Shivaram Venkataraman] Merge pull request #208 from lythesia/master
b317aa7 [Zongheng Yang] Merge pull request #243 from hqzizania/master
136a07e [Zongheng Yang] Merge pull request #242 from hqzizania/stats
cd66603 [cafreeman] new line at EOF
8b76e81 [Shivaram Venkataraman] Merge pull request #233 from redbaron/fail-early-on-missing-dep
7dd81b7 [cafreeman] Documentation
0e2a94f [cafreeman] Define functions for schema and fields
Diffstat (limited to 'core/src')
-rw-r--r-- | core/src/main/scala/org/apache/spark/api/r/RRDD.scala | 131 | ||||
-rw-r--r-- | core/src/main/scala/org/apache/spark/api/r/SerDe.scala | 14 |
2 files changed, 76 insertions, 69 deletions
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 5fa4d483b8..6fea5e1144 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 @@ -42,10 +42,15 @@ private abstract class BaseRRDD[T: ClassTag, U: ClassTag]( rLibDir: String, 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 + // The parent may be also an RRDD, so we should launch it first. val parentIterator = firstParent[T].iterator(partition, context) @@ -69,7 +74,7 @@ private abstract class BaseRRDD[T: ClassTag, U: ClassTag]( // the socket used to receive the output of task val outSocket = serverSocket.accept() val inputStream = new BufferedInputStream(outSocket.getInputStream) - val dataStream = openDataStream(inputStream) + dataStream = new DataInputStream(inputStream) serverSocket.close() try { @@ -155,6 +160,7 @@ private abstract class BaseRRDD[T: ClassTag, U: ClassTag]( } else if (deserializer == SerializationFormats.ROW) { dataOut.write(elem.asInstanceOf[Array[Byte]]) } else if (deserializer == SerializationFormats.STRING) { + // write string(for StringRRDD) printOut.println(elem) } } @@ -180,9 +186,41 @@ private abstract class BaseRRDD[T: ClassTag, U: ClassTag]( }.start() } - protected def openDataStream(input: InputStream): Closeable + protected def readData(length: Int): U - protected def read(): 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) + } + } } /** @@ -202,31 +240,16 @@ private class PairwiseRRDD[T: ClassTag]( SerializationFormats.BYTE, packageNames, rLibDir, broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) { - private var dataStream: DataInputStream = _ - - override protected def openDataStream(input: InputStream): Closeable = { - dataStream = new DataInputStream(input) - dataStream - } - - override protected def read(): (Int, Array[Byte]) = { - try { - val length = dataStream.readInt() - - 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 // End of input - } - } catch { - case eof: EOFException => { - throw new SparkException("R worker exited unexpectedly (crashed)", eof) - } - } + 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) @@ -247,28 +270,13 @@ private class RRDD[T: ClassTag]( parent, -1, func, deserializer, serializer, packageNames, rLibDir, broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) { - private var dataStream: DataInputStream = _ - - override protected def openDataStream(input: InputStream): Closeable = { - dataStream = new DataInputStream(input) - dataStream - } - - override protected def read(): Array[Byte] = { - try { - val length = dataStream.readInt() - - length match { - case length if length > 0 => - val obj = new Array[Byte](length) - dataStream.readFully(obj, 0, length) - obj - case _ => null - } - } catch { - case eof: EOFException => { - throw new SparkException("R worker exited unexpectedly (crashed)", eof) - } + 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 } } @@ -289,26 +297,21 @@ private class StringRRDD[T: ClassTag]( parent, -1, func, deserializer, SerializationFormats.STRING, packageNames, rLibDir, broadcastVars.map(x => x.asInstanceOf[Broadcast[Object]])) { - private var dataStream: BufferedReader = _ - - override protected def openDataStream(input: InputStream): Closeable = { - dataStream = new BufferedReader(new InputStreamReader(input)) - dataStream - } - - override protected def read(): String = { - try { - dataStream.readLine() - } catch { - case e: IOException => { - throw new SparkException("R worker exited unexpectedly (crashed)", e) - } + 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, diff --git a/core/src/main/scala/org/apache/spark/api/r/SerDe.scala b/core/src/main/scala/org/apache/spark/api/r/SerDe.scala index ccb2a371f4..371dfe454d 100644 --- a/core/src/main/scala/org/apache/spark/api/r/SerDe.scala +++ b/core/src/main/scala/org/apache/spark/api/r/SerDe.scala @@ -85,13 +85,17 @@ private[spark] object SerDe { in.readDouble() } + def readStringBytes(in: DataInputStream, len: Int): String = { + val bytes = new Array[Byte](len) + in.readFully(bytes) + assert(bytes(len - 1) == 0) + val str = new String(bytes.dropRight(1), "UTF-8") + str + } + def readString(in: DataInputStream): String = { val len = in.readInt() - val asciiBytes = new Array[Byte](len) - in.readFully(asciiBytes) - assert(asciiBytes(len - 1) == 0) - val str = new String(asciiBytes.dropRight(1).map(_.toChar)) - str + readStringBytes(in, len) } def readBoolean(in: DataInputStream): Boolean = { |