[SPARK-13902][SCHEDULER] Make DAGScheduler not to create duplicate stage.

## What changes were proposed in this pull request?

`DAGScheduler`sometimes generate incorrect stage graph.

Suppose you have the following DAG:

```
[A] <--(s_A)-- [B] <--(s_B)-- [C] <--(s_C)-- [D]
            \                /
              <-------------
```

Note: [] means an RDD, () means a shuffle dependency.

Here, RDD `B` has a shuffle dependency on RDD `A`, and RDD `C` has shuffle dependency on both `B` and `A`. The shuffle dependency IDs are numbers in the `DAGScheduler`, but to make the example easier to understand, let's call the shuffled data from `A` shuffle dependency ID `s_A` and the shuffled data from `B` shuffle dependency ID `s_B`.
The `getAncestorShuffleDependencies` method in `DAGScheduler` (incorrectly) does not check for duplicates when it's adding ShuffleDependencies to the parents data structure, so for this DAG, when `getAncestorShuffleDependencies` gets called on `C` (previous of the final RDD), `getAncestorShuffleDependencies` will return `s_A`, `s_B`, `s_A` (`s_A` gets added twice: once when the method "visit"s RDD `C`, and once when the method "visit"s RDD `B`). This is problematic because this line of code: https://github.com/apache/spark/blob/8ef3399/core/src/main/scala/org/apache/spark/scheduler/DAGScheduler.scala#L289 then generates a new shuffle stage for each dependency returned by `getAncestorShuffleDependencies`, resulting in duplicate map stages that compute the map output from RDD `A`.

As a result, `DAGScheduler` generates the following stages and their parents for each shuffle:

| | stage | parents |
|----|----|----|
| s_A | ShuffleMapStage 2 | List() |
| s_B | ShuffleMapStage 1 | List(ShuffleMapStage 0) |
| s_C | ShuffleMapStage 3 | List(ShuffleMapStage 1, ShuffleMapStage 2) |
| - | ResultStage 4 | List(ShuffleMapStage 3) |

The stage for s_A should be `ShuffleMapStage 0`, but the stage for `s_A` is generated twice as `ShuffleMapStage 2` and `ShuffleMapStage 0` is overwritten by `ShuffleMapStage 2`, and the stage `ShuffleMap Stage1` keeps referring the old stage `ShuffleMapStage 0`.

This patch is fixing it.

## How was this patch tested?

I added the sample RDD graph to show the illegal stage graph to `DAGSchedulerSuite`.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #12655 from ueshin/issues/SPARK-13902.

Author: ueshin

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

@@ -286,7 +286,9 @@ class DAGScheduler(
       case None =>
         // We are going to register ancestor shuffle dependencies
         getAncestorShuffleDependencies(shuffleDep.rdd).foreach { dep =>
-          shuffleToMapStage(dep.shuffleId) = newOrUsedShuffleStage(dep, firstJobId)
+          if (!shuffleToMapStage.contains(dep.shuffleId)) {
+            shuffleToMapStage(dep.shuffleId) = newOrUsedShuffleStage(dep, firstJobId)
+          }
         }
         // Then register current shuffleDep
         val stage = newOrUsedShuffleStage(shuffleDep, firstJobId)

core/src/test/scala/org/apache/spark/scheduler/DAGSchedulerSuite.scala

@@ -325,6 +325,53 @@ class DAGSchedulerSuite extends SparkFunSuite with LocalSparkContext with Timeou
     assert(sparkListener.stageByOrderOfExecution(0) < sparkListener.stageByOrderOfExecution(1))
   }
 
+  /**
+   * This test ensures that DAGScheduler build stage graph correctly.
+   *
+   * Suppose you have the following DAG:
+   *
+   * [A] <--(s_A)-- [B] <--(s_B)-- [C] <--(s_C)-- [D]
+   *             \                /
+   *               <-------------
+   *
+   * Here, RDD B has a shuffle dependency on RDD A, and RDD C has shuffle dependency on both
+   * B and A. The shuffle dependency IDs are numbers in the DAGScheduler, but to make the example
+   * easier to understand, let's call the shuffled data from A shuffle dependency ID s_A and the
+   * shuffled data from B shuffle dependency ID s_B.
+   *
+   * Note: [] means an RDD, () means a shuffle dependency.
+   */
+  test("[SPARK-13902] Ensure no duplicate stages are created") {
+    val rddA = new MyRDD(sc, 1, Nil)
+    val shuffleDepA = new ShuffleDependency(rddA, new HashPartitioner(1))
+    val s_A = shuffleDepA.shuffleId
+
+    val rddB = new MyRDD(sc, 1, List(shuffleDepA), tracker = mapOutputTracker)
+    val shuffleDepB = new ShuffleDependency(rddB, new HashPartitioner(1))
+    val s_B = shuffleDepB.shuffleId
+
+    val rddC = new MyRDD(sc, 1, List(shuffleDepA, shuffleDepB), tracker = mapOutputTracker)
+    val shuffleDepC = new ShuffleDependency(rddC, new HashPartitioner(1))
+    val s_C = shuffleDepC.shuffleId
+
+    val rddD = new MyRDD(sc, 1, List(shuffleDepC), tracker = mapOutputTracker)
+
+    submit(rddD, Array(0))
+
+    assert(scheduler.shuffleToMapStage.size === 3)
+    assert(scheduler.activeJobs.size === 1)
+
+    val mapStageA = scheduler.shuffleToMapStage(s_A)
+    val mapStageB = scheduler.shuffleToMapStage(s_B)
+    val mapStageC = scheduler.shuffleToMapStage(s_C)
+    val finalStage = scheduler.activeJobs.head.finalStage
+
+    assert(mapStageA.parents.isEmpty)
+    assert(mapStageB.parents === List(mapStageA))
+    assert(mapStageC.parents === List(mapStageA, mapStageB))
+    assert(finalStage.parents === List(mapStageC))
+  }
+
   test("zero split job") {
     var numResults = 0
     var failureReason: Option[Exception] = None