Merge pull request alteryx#41 from pwendell/shuffle-benchmark

Provide Instrumentation for Shuffle Write Performance

Shuffle write performance can have a major impact on the performance of jobs. This patch adds a few pieces of instrumentation related to shuffle writes. They are:

1. A listing of the time spent performing blocking writes for each task. This is implemented by keeping track of the aggregate delay seen by many individual writes.
2. An undocumented option `spark.shuffle.sync` which forces shuffle data to sync to disk. This is necessary for measuring shuffle performance in the absence of the OS buffer cache.
3. An internal utility which micro-benchmarks write throughput for simulated shuffle outputs.

I'm going to do some performance testing on this to see whether these small timing calls add overhead. From a feature perspective, however, I consider this complete. Any feedback is appreciated.
(cherry picked from commit 35886f3)

Signed-off-by: Patrick Wendell <[email protected]>

core/src/main/scala/org/apache/spark/executor/TaskMetrics.scala

@@ -102,4 +102,9 @@ class ShuffleWriteMetrics extends Serializable {
    * Number of bytes written for a shuffle
    */
   var shuffleBytesWritten: Long = _
+
+  /**
+   * Time spent blocking on writes to disk or buffer cache, in nanoseconds.
+   */
+  var shuffleWriteTime: Long = _
 }

core/src/main/scala/org/apache/spark/scheduler/ShuffleMapTask.scala

@@ -164,17 +164,20 @@ private[spark] class ShuffleMapTask(
 
       // Commit the writes. Get the size of each bucket block (total block size).
       var totalBytes = 0L
+      var totalTime = 0L
       val compressedSizes: Array[Byte] = buckets.writers.map { writer: BlockObjectWriter =>
         writer.commit()
         writer.close()
         val size = writer.size()
         totalBytes += size
+        totalTime += writer.timeWriting()
         MapOutputTracker.compressSize(size)
       }
 
       // Update shuffle metrics.
       val shuffleMetrics = new ShuffleWriteMetrics
       shuffleMetrics.shuffleBytesWritten = totalBytes
+      shuffleMetrics.shuffleWriteTime = totalTime
       metrics.get.shuffleWriteMetrics = Some(shuffleMetrics)
 
       new MapStatus(blockManager.blockManagerId, compressedSizes)

core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala

@@ -62,4 +62,9 @@ abstract class BlockObjectWriter(val blockId: BlockId) {
    * Size of the valid writes, in bytes.
    */
   def size(): Long
+
+  /**
+   * Cumulative time spent performing blocking writes, in ns.
+   */
+  def timeWriting(): Long
 }

core/src/main/scala/org/apache/spark/storage/DiskStore.scala

@@ -45,29 +45,64 @@ private class DiskStore(blockManager: BlockManager, rootDirs: String)
   class DiskBlockObjectWriter(blockId: BlockId, serializer: Serializer, bufferSize: Int)
     extends BlockObjectWriter(blockId) {
 
+    /** Intercepts write calls and tracks total time spent writing. Not thread safe. */
+    private class TimeTrackingOutputStream(out: OutputStream) extends OutputStream {
+      def timeWriting = _timeWriting
+      private var _timeWriting = 0L
+
+      private def callWithTiming(f: => Unit) = {
+        val start = System.nanoTime()
+        f
+        _timeWriting += (System.nanoTime() - start)
+      }
+
+      def write(i: Int): Unit = callWithTiming(out.write(i))
+      override def write(b: Array[Byte]) = callWithTiming(out.write(b))
+      override def write(b: Array[Byte], off: Int, len: Int) = callWithTiming(out.write(b, off, len))
+    }
+
     private val f: File = createFile(blockId /*, allowAppendExisting */)
+    private val syncWrites = System.getProperty("spark.shuffle.sync", "false").toBoolean
 
     // The file channel, used for repositioning / truncating the file.
     private var channel: FileChannel = null
     private var bs: OutputStream = null
+    private var fos: FileOutputStream = null
+    private var ts: TimeTrackingOutputStream = null
     private var objOut: SerializationStream = null
     private var lastValidPosition = 0L
     private var initialized = false
+    private var _timeWriting = 0L
 
     override def open(): DiskBlockObjectWriter = {
-      val fos = new FileOutputStream(f, true)
+      fos = new FileOutputStream(f, true)
+      ts = new TimeTrackingOutputStream(fos)
       channel = fos.getChannel()
-      bs = blockManager.wrapForCompression(blockId, new FastBufferedOutputStream(fos, bufferSize))
+      bs = blockManager.wrapForCompression(blockId, new FastBufferedOutputStream(ts, bufferSize))
       objOut = serializer.newInstance().serializeStream(bs)
       initialized = true
       this
     }
 
     override def close() {
       if (initialized) {
-        objOut.close()
+        if (syncWrites) {
+          // Force outstanding writes to disk and track how long it takes
+          objOut.flush()
+          val start = System.nanoTime()
+          fos.getFD.sync()
+          _timeWriting += System.nanoTime() - start
+          objOut.close()
+        } else {
+          objOut.close()
+        }
+
+        _timeWriting += ts.timeWriting
+
         channel = null
         bs = null
+        fos = null
+        ts = null
         objOut = null
       }
       // Invoke the close callback handler.
@@ -110,6 +145,9 @@ private class DiskStore(blockManager: BlockManager, rootDirs: String)
     }
 
     override def size(): Long = lastValidPosition
+
+    // Only valid if called after close()
+    override def timeWriting = _timeWriting
   }
 
   private val MAX_DIR_CREATION_ATTEMPTS: Int = 10

core/src/main/scala/org/apache/spark/ui/jobs/StagePage.scala

@@ -86,7 +86,7 @@ private[spark] class StagePage(parent: JobProgressUI) {
         Seq("Task ID", "Status", "Locality Level", "Executor", "Launch Time", "Duration") ++
         Seq("GC Time") ++
         {if (hasShuffleRead) Seq("Shuffle Read")  else Nil} ++
-        {if (hasShuffleWrite) Seq("Shuffle Write") else Nil} ++
+        {if (hasShuffleWrite) Seq("Write Time", "Shuffle Write") else Nil} ++
         Seq("Errors")
 
       val taskTable = listingTable(taskHeaders, taskRow(hasShuffleRead, hasShuffleWrite), tasks)
@@ -169,6 +169,8 @@ private[spark] class StagePage(parent: JobProgressUI) {
           Utils.bytesToString(s.remoteBytesRead)}.getOrElse("")}</td>
       }}
       {if (shuffleWrite) {
+      <td>{metrics.flatMap{m => m.shuffleWriteMetrics}.map{s =>
+        parent.formatDuration(s.shuffleWriteTime / (1000 * 1000))}.getOrElse("")}</td>
         <td>{metrics.flatMap{m => m.shuffleWriteMetrics}.map{s =>
           Utils.bytesToString(s.shuffleBytesWritten)}.getOrElse("")}</td>
       }}

core/src/main/scala/spark/storage/StoragePerfTester.scala

@@ -0,0 +1,84 @@
+package org.apache.spark.storage
+
+import java.util.concurrent.atomic.AtomicLong
+import java.util.concurrent.{CountDownLatch, Executors}
+
+import org.apache.spark.serializer.KryoSerializer
+import org.apache.spark.SparkContext
+import org.apache.spark.util.Utils
+
+/** Utility for micro-benchmarking shuffle write performance.
+  *
+  * Writes simulated shuffle output from several threads and records the observed throughput*/
+object StoragePerfTester {
+  def main(args: Array[String]) = {
+    /** Total amount of data to generate. Distributed evenly amongst maps and reduce splits. */
+    val dataSizeMb = Utils.memoryStringToMb(sys.env.getOrElse("OUTPUT_DATA", "1g"))
+
+    /** Number of map tasks. All tasks execute concurrently. */
+    val numMaps = sys.env.get("NUM_MAPS").map(_.toInt).getOrElse(8)
+
+    /** Number of reduce splits for each map task. */
+    val numOutputSplits = sys.env.get("NUM_REDUCERS").map(_.toInt).getOrElse(500)
+
+    val recordLength = 1000 // ~1KB records
+    val totalRecords = dataSizeMb * 1000
+    val recordsPerMap = totalRecords / numMaps
+
+    val writeData = "1" * recordLength
+    val executor = Executors.newFixedThreadPool(numMaps)
+
+    System.setProperty("spark.shuffle.compress", "false")
+    System.setProperty("spark.shuffle.sync", "true")
+
+    // This is only used to instantiate a BlockManager. All thread scheduling is done manually.
+    val sc = new SparkContext("local[4]", "Write Tester")
+    val blockManager = sc.env.blockManager
+
+    def writeOutputBytes(mapId: Int, total: AtomicLong) = {
+      val shuffle = blockManager.shuffleBlockManager.forShuffle(1, numOutputSplits,
+        new KryoSerializer())
+      val buckets = shuffle.acquireWriters(mapId)
+      for (i <- 1 to recordsPerMap) {
+        buckets.writers(i % numOutputSplits).write(writeData)
+      }
+      buckets.writers.map {w =>
+        w.commit()
+        total.addAndGet(w.size())
+        w.close()
+      }
+
+      shuffle.releaseWriters(buckets)
+    }
+
+    val start = System.currentTimeMillis()
+    val latch = new CountDownLatch(numMaps)
+    val totalBytes = new AtomicLong()
+    for (task <- 1 to numMaps) {
+      executor.submit(new Runnable() {
+        override def run() = {
+          try {
+            writeOutputBytes(task, totalBytes)
+            latch.countDown()
+          } catch {
+            case e: Exception =>
+              println("Exception in child thread: " + e + " " + e.getMessage)
+              System.exit(1)
+          }
+        }
+      })
+    }
+    latch.await()
+    val end = System.currentTimeMillis()
+    val time = (end - start) / 1000.0
+    val bytesPerSecond = totalBytes.get() / time
+    val bytesPerFile = (totalBytes.get() / (numOutputSplits * numMaps.toDouble)).toLong
+
+    System.err.println("files_total\t\t%s".format(numMaps * numOutputSplits))
+    System.err.println("bytes_per_file\t\t%s".format(Utils.bytesToString(bytesPerFile)))
+    System.err.println("agg_throughput\t\t%s/s".format(Utils.bytesToString(bytesPerSecond.toLong)))
+
+    executor.shutdown()
+    sc.stop()
+  }
+}