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From pwend...@apache.org
Subject [46/50] git commit: Defensively allocate memory from global pool
Date Sat, 11 Jan 2014 00:26:03 GMT
Defensively allocate memory from global pool

This is an alternative to the existing approach, which evenly distributes the
collective shuffle memory among all running tasks. In the new approach, each
thread requests a chunk of memory whenever its map is about to multiplicatively
grow. If there is sufficient memory in the global pool, the thread allocates it
and grows its map. Otherwise, it spills.

A danger with the previous approach is that a new task may quickly fill up its
map before old tasks finish spilling, potentially causing an OOM. This approach
prevents this scenario as it favors existing tasks over new tasks; any thread
that may step over the boundary of other threads defensively backs off and
starts spilling.

Testing through spark-perf reveals: (1) When no spills have occured, the
performance of external sorting using this memory management approach is
essentially the same as without external sorting. (2) When one or more spills
have occured, the performance of external sorting is a small multiple (3x) worse


Project: http://git-wip-us.apache.org/repos/asf/incubator-spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-spark/commit/aa5002bb
Tree: http://git-wip-us.apache.org/repos/asf/incubator-spark/tree/aa5002bb
Diff: http://git-wip-us.apache.org/repos/asf/incubator-spark/diff/aa5002bb

Branch: refs/heads/master
Commit: aa5002bb9682ae6271db1fedb2c2658ed04fd4a1
Parents: d76e1f9
Author: Andrew Or <andrewor14@gmail.com>
Authored: Thu Jan 9 21:43:58 2014 -0800
Committer: Andrew Or <andrewor14@gmail.com>
Committed: Thu Jan 9 21:43:58 2014 -0800

----------------------------------------------------------------------
 .../main/scala/org/apache/spark/SparkEnv.scala  | 18 ++--
 .../org/apache/spark/executor/Executor.scala    |  7 +-
 .../spark/storage/BlockObjectWriter.scala       |  4 +
 .../spark/util/collection/AppendOnlyMap.scala   | 12 ++-
 .../util/collection/ExternalAppendOnlyMap.scala | 86 +++++++++++++-------
 5 files changed, 80 insertions(+), 47 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-spark/blob/aa5002bb/core/src/main/scala/org/apache/spark/SparkEnv.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/SparkEnv.scala b/core/src/main/scala/org/apache/spark/SparkEnv.scala
index 584261d..08b592d 100644
--- a/core/src/main/scala/org/apache/spark/SparkEnv.scala
+++ b/core/src/main/scala/org/apache/spark/SparkEnv.scala
@@ -17,8 +17,6 @@
 
 package org.apache.spark
 
-import java.util.concurrent.atomic.AtomicInteger
-
 import scala.collection.mutable
 import scala.concurrent.Await
 
@@ -56,12 +54,13 @@ class SparkEnv private[spark] (
     val httpFileServer: HttpFileServer,
     val sparkFilesDir: String,
     val metricsSystem: MetricsSystem,
-    val conf: SparkConf) {
+    val conf: SparkConf) extends Logging {
 
-  private val pythonWorkers = mutable.HashMap[(String, Map[String, String]), PythonWorkerFactory]()
+  // A mapping of thread ID to amount of memory used for shuffle in bytes
+  // All accesses should be manually synchronized
+  val shuffleMemoryMap = mutable.HashMap[Long, Long]()
 
-  // Number of tasks currently running across all threads
-  private val _numRunningTasks = new AtomicInteger(0)
+  private val pythonWorkers = mutable.HashMap[(String, Map[String, String]), PythonWorkerFactory]()
 
   // A general, soft-reference map for metadata needed during HadoopRDD split computation
   // (e.g., HadoopFileRDD uses this to cache JobConfs and InputFormats).
@@ -90,13 +89,6 @@ class SparkEnv private[spark] (
       pythonWorkers.getOrElseUpdate(key, new PythonWorkerFactory(pythonExec, envVars)).create()
     }
   }
-
-  /**
-   * Return the number of tasks currently running across all threads
-   */
-  def numRunningTasks: Int = _numRunningTasks.intValue()
-  def incrementNumRunningTasks(): Int = _numRunningTasks.incrementAndGet()
-  def decrementNumRunningTasks(): Int = _numRunningTasks.decrementAndGet()
 }
 
 object SparkEnv extends Logging {

http://git-wip-us.apache.org/repos/asf/incubator-spark/blob/aa5002bb/core/src/main/scala/org/apache/spark/executor/Executor.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/executor/Executor.scala b/core/src/main/scala/org/apache/spark/executor/Executor.scala
index bd202af..a7b2328 100644
--- a/core/src/main/scala/org/apache/spark/executor/Executor.scala
+++ b/core/src/main/scala/org/apache/spark/executor/Executor.scala
@@ -186,7 +186,6 @@ private[spark] class Executor(
       var taskStart: Long = 0
       def gcTime = ManagementFactory.getGarbageCollectorMXBeans.map(_.getCollectionTime).sum
       val startGCTime = gcTime
-      env.incrementNumRunningTasks()
 
       try {
         SparkEnv.set(env)
@@ -280,7 +279,11 @@ private[spark] class Executor(
           //System.exit(1)
         }
       } finally {
-        env.decrementNumRunningTasks()
+        // TODO: Unregister shuffle memory only for ShuffleMapTask
+        val shuffleMemoryMap = env.shuffleMemoryMap
+        shuffleMemoryMap.synchronized {
+          shuffleMemoryMap.remove(Thread.currentThread().getId)
+        }
         runningTasks.remove(taskId)
       }
     }

http://git-wip-us.apache.org/repos/asf/incubator-spark/blob/aa5002bb/core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala b/core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala
index 61e63c6..369a277 100644
--- a/core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala
+++ b/core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala
@@ -181,4 +181,8 @@ class DiskBlockObjectWriter(
 
   // Only valid if called after close()
   override def timeWriting() = _timeWriting
+
+  def bytesWritten: Long = {
+    lastValidPosition - initialPosition
+  }
 }

http://git-wip-us.apache.org/repos/asf/incubator-spark/blob/aa5002bb/core/src/main/scala/org/apache/spark/util/collection/AppendOnlyMap.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/util/collection/AppendOnlyMap.scala b/core/src/main/scala/org/apache/spark/util/collection/AppendOnlyMap.scala
index 6faaa31..d98c7aa 100644
--- a/core/src/main/scala/org/apache/spark/util/collection/AppendOnlyMap.scala
+++ b/core/src/main/scala/org/apache/spark/util/collection/AppendOnlyMap.scala
@@ -30,14 +30,15 @@ import java.util.{Arrays, Comparator}
  * TODO: Cache the hash values of each key? java.util.HashMap does that.
  */
 private[spark]
-class AppendOnlyMap[K, V](initialCapacity: Int = 64) extends Iterable[(K, V)] with Serializable
{
+class AppendOnlyMap[K, V](initialCapacity: Int = 64) extends Iterable[(K,
+  V)] with Serializable {
   require(initialCapacity <= (1 << 29), "Can't make capacity bigger than 2^29 elements")
   require(initialCapacity >= 1, "Invalid initial capacity")
 
   private var capacity = nextPowerOf2(initialCapacity)
   private var mask = capacity - 1
   private var curSize = 0
-  private var growThreshold = LOAD_FACTOR * capacity
+  private var growThreshold = (LOAD_FACTOR * capacity).toInt
 
   // Holds keys and values in the same array for memory locality; specifically, the order
of
   // elements is key0, value0, key1, value1, key2, value2, etc.
@@ -239,7 +240,7 @@ class AppendOnlyMap[K, V](initialCapacity: Int = 64) extends Iterable[(K,
V)] wi
     data = newData
     capacity = newCapacity
     mask = newMask
-    growThreshold = LOAD_FACTOR * newCapacity
+    growThreshold = (LOAD_FACTOR * newCapacity).toInt
   }
 
   private def nextPowerOf2(n: Int): Int = {
@@ -288,4 +289,9 @@ class AppendOnlyMap[K, V](initialCapacity: Int = 64) extends Iterable[(K,
V)] wi
       }
     }
   }
+
+  /**
+   * Return whether the next insert will cause the map to grow
+   */
+  def atGrowThreshold: Boolean = curSize == growThreshold
 }

http://git-wip-us.apache.org/repos/asf/incubator-spark/blob/aa5002bb/core/src/main/scala/org/apache/spark/util/collection/ExternalAppendOnlyMap.scala
----------------------------------------------------------------------
diff --git a/core/src/main/scala/org/apache/spark/util/collection/ExternalAppendOnlyMap.scala
b/core/src/main/scala/org/apache/spark/util/collection/ExternalAppendOnlyMap.scala
index a5897e8..50f0535 100644
--- a/core/src/main/scala/org/apache/spark/util/collection/ExternalAppendOnlyMap.scala
+++ b/core/src/main/scala/org/apache/spark/util/collection/ExternalAppendOnlyMap.scala
@@ -22,14 +22,16 @@ import java.util.Comparator
 
 import it.unimi.dsi.fastutil.io.FastBufferedInputStream
 
-import scala.collection.mutable.{ArrayBuffer, PriorityQueue}
+import scala.collection.mutable
+import scala.collection.mutable.ArrayBuffer
 
 import org.apache.spark.{Logging, SparkEnv}
 import org.apache.spark.serializer.Serializer
 import org.apache.spark.storage.{DiskBlockManager, DiskBlockObjectWriter}
 
 /**
- * An append-only map that spills sorted content to disk when the memory threshold is exceeded.
+ * An append-only map that spills sorted content to disk when there is insufficient space
for it
+ * to grow.
  *
  * This map takes two passes over the data:
  *
@@ -42,7 +44,7 @@ import org.apache.spark.storage.{DiskBlockManager, DiskBlockObjectWriter}
  * writes. This may lead to a performance regression compared to the normal case of using
the
  * non-spilling AppendOnlyMap.
  *
- * A few parameters control the memory threshold:
+ * Two parameters control the memory threshold:
  *
  *   `spark.shuffle.memoryFraction` specifies the collective amount of memory used for storing
  *   these maps as a fraction of the executor's total memory. Since each concurrently running
@@ -51,9 +53,6 @@ import org.apache.spark.storage.{DiskBlockManager, DiskBlockObjectWriter}
  *
  *   `spark.shuffle.safetyFraction` specifies an additional margin of safety as a fraction
of
  *   this threshold, in case map size estimation is not sufficiently accurate.
- *
- *   `spark.shuffle.updateThresholdInterval` controls how frequently each thread checks on
- *   shared executor state to update its local memory threshold.
  */
 
 private[spark] class ExternalAppendOnlyMap[K, V, C](
@@ -77,12 +76,9 @@ private[spark] class ExternalAppendOnlyMap[K, V, C](
     (Runtime.getRuntime.maxMemory * memoryFraction * safetyFraction).toLong
   }
 
-  // Maximum size for this map before a spill is triggered
-  private var spillThreshold = maxMemoryThreshold
-
-  // How often to update spillThreshold
-  private val updateThresholdInterval =
-    sparkConf.getInt("spark.shuffle.updateThresholdInterval", 100)
+  // How many inserts into this map before tracking its shuffle memory usage
+  private val initialInsertThreshold =
+    sparkConf.getLong("spark.shuffle.initialInsertThreshold", 1000)
 
   private val fileBufferSize = sparkConf.getInt("spark.shuffle.file.buffer.kb", 100) * 1024
   private val syncWrites = sparkConf.get("spark.shuffle.sync", "false").toBoolean
@@ -91,30 +87,54 @@ private[spark] class ExternalAppendOnlyMap[K, V, C](
   private var insertCount = 0
   private var spillCount = 0
 
+  /**
+   * Insert the given key and value into the map.
+   *
+   * If the underlying map is about to grow, check if the global pool of shuffle memory has
+   * enough room for this to happen. If so, allocate the memory required to grow the map;
+   * otherwise, spill the in-memory map to disk.
+   *
+   * The shuffle memory usage of the first initialInsertThreshold entries is not tracked.
+   */
   def insert(key: K, value: V) {
     insertCount += 1
     val update: (Boolean, C) => C = (hadVal, oldVal) => {
       if (hadVal) mergeValue(oldVal, value) else createCombiner(value)
     }
-    currentMap.changeValue(key, update)
-    if (insertCount % updateThresholdInterval == 1) {
-      updateSpillThreshold()
-    }
-    if (currentMap.estimateSize() > spillThreshold) {
-      spill()
+    if (insertCount > initialInsertThreshold && currentMap.atGrowThreshold) {
+      val mapSize = currentMap.estimateSize()
+      var shouldSpill = false
+      val shuffleMemoryMap = SparkEnv.get.shuffleMemoryMap
+
+      // Atomically check whether there is sufficient memory in the global pool for
+      // this map to grow and, if possible, allocate the required amount
+      shuffleMemoryMap.synchronized {
+        val threadId = Thread.currentThread().getId
+        val previouslyOccupiedMemory = shuffleMemoryMap.get(threadId)
+        val availableMemory = maxMemoryThreshold -
+          (shuffleMemoryMap.values.sum - previouslyOccupiedMemory.getOrElse(0L))
+
+        // Assume map grow factor is 2x
+        shouldSpill = availableMemory < mapSize * 2
+        if (!shouldSpill) {
+          shuffleMemoryMap(threadId) = mapSize * 2
+        }
+      }
+      // Do not synchronize spills
+      if (shouldSpill) {
+        spill(mapSize)
+      }
     }
+    currentMap.changeValue(key, update)
   }
 
-  // TODO: differentiate ShuffleMapTask's from ResultTask's
-  private def updateSpillThreshold() {
-    val numRunningTasks = math.max(SparkEnv.get.numRunningTasks, 1)
-    spillThreshold = maxMemoryThreshold / numRunningTasks
-  }
-
-  private def spill() {
+  /**
+   * Sort the existing contents of the in-memory map and spill them to a temporary file on
disk
+   */
+  private def spill(mapSize: Long) {
     spillCount += 1
-    logWarning("In-memory map exceeded %s MB! Spilling to disk (%d time%s so far)"
-      .format(spillThreshold / (1024 * 1024), spillCount, if (spillCount > 1) "s" else
""))
+    logWarning("* Spilling in-memory map of %d MB to disk (%d time%s so far)"
+      .format(mapSize / (1024 * 1024), spillCount, if (spillCount > 1) "s" else ""))
     val (blockId, file) = diskBlockManager.createTempBlock()
     val writer =
       new DiskBlockObjectWriter(blockId, file, serializer, fileBufferSize, identity, syncWrites)
@@ -131,6 +151,13 @@ private[spark] class ExternalAppendOnlyMap[K, V, C](
     }
     currentMap = new SizeTrackingAppendOnlyMap[K, C]
     spilledMaps.append(new DiskMapIterator(file))
+
+    // Reset the amount of shuffle memory used by this map in the global pool
+    val shuffleMemoryMap = SparkEnv.get.shuffleMemoryMap
+    shuffleMemoryMap.synchronized {
+      shuffleMemoryMap(Thread.currentThread().getId) = 0
+    }
+    insertCount = 0
   }
 
   override def iterator: Iterator[(K, C)] = {
@@ -145,11 +172,12 @@ private[spark] class ExternalAppendOnlyMap[K, V, C](
   private class ExternalIterator extends Iterator[(K, C)] {
 
     // A fixed-size queue that maintains a buffer for each stream we are currently merging
-    val mergeHeap = new PriorityQueue[StreamBuffer]
+    val mergeHeap = new mutable.PriorityQueue[StreamBuffer]
 
     // Input streams are derived both from the in-memory map and spilled maps on disk
     // The in-memory map is sorted in place, while the spilled maps are already in sorted
order
-    val inputStreams = Seq(currentMap.destructiveSortedIterator(comparator)) ++ spilledMaps
+    val sortedMap = currentMap.destructiveSortedIterator(comparator)
+    val inputStreams = Seq(sortedMap) ++ spilledMaps
 
     inputStreams.foreach{ it =>
       val kcPairs = getMorePairs(it)


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