[SPARK-16414][YARN] Fix bugs for "Can not get user config when calling...

[SPARK-16414][YARN] Fix bugs for "Can not get user config when calling SparkHadoopUtil.get.conf on yarn cluser mode"

## What changes were proposed in this pull request?

The `SparkHadoopUtil` singleton was instantiated before `ApplicationMaster` in `ApplicationMaster.main` when deploying spark on yarn cluster mode, the `conf` in the `SparkHadoopUtil` singleton didn't include user's configuration.

So, we should load the properties file with the Spark configuration and set entries as system properties before `SparkHadoopUtil` first instantiate.

## How was this patch tested?

Add a test case

Author: sharkd <sharkd.tu@gmail.com>
Author: sharkdtu <sharkdtu@tencent.com>

Closes #14088 from sharkdtu/master.

yarn/src/main/scala/org/apache/spark/deploy/yarn/ApplicationMaster.scala

@@ -50,14 +50,6 @@ private[spark] class ApplicationMaster(
     client: YarnRMClient)
   extends Logging {
 
-  // Load the properties file with the Spark configuration and set entries as system properties,
-  // so that user code run inside the AM also has access to them.
-  if (args.propertiesFile != null) {
-    Utils.getPropertiesFromFile(args.propertiesFile).foreach { case (k, v) =>
-      sys.props(k) = v
-    }
-  }
-
   // TODO: Currently, task to container is computed once (TaskSetManager) - which need not be
   // optimal as more containers are available. Might need to handle this better.
 
@@ -743,6 +735,15 @@ object ApplicationMaster extends Logging {
   def main(args: Array[String]): Unit = {
     SignalUtils.registerLogger(log)
     val amArgs = new ApplicationMasterArguments(args)
+
+    // Load the properties file with the Spark configuration and set entries as system properties,
+    // so that user code run inside the AM also has access to them.
+    // Note: we must do this before SparkHadoopUtil instantiated
+    if (amArgs.propertiesFile != null) {
+      Utils.getPropertiesFromFile(amArgs.propertiesFile).foreach { case (k, v) =>
+        sys.props(k) = v
+      }
+    }
     SparkHadoopUtil.get.runAsSparkUser { () =>
       master = new ApplicationMaster(amArgs, new YarnRMClient)
       System.exit(master.run())

yarn/src/test/scala/org/apache/spark/deploy/yarn/YarnClusterSuite.scala

@@ -32,6 +32,7 @@ import org.scalatest.Matchers
 import org.scalatest.concurrent.Eventually._
 
 import org.apache.spark._
+import org.apache.spark.deploy.SparkHadoopUtil
 import org.apache.spark.internal.Logging
 import org.apache.spark.launcher._
 import org.apache.spark.scheduler.{SparkListener, SparkListenerApplicationStart,
@@ -106,6 +107,10 @@ class YarnClusterSuite extends BaseYarnClusterSuite {
       ))
   }
 
+  test("run Spark in yarn-cluster mode with using SparkHadoopUtil.conf") {
+    testYarnAppUseSparkHadoopUtilConf()
+  }
+
   test("run Spark in yarn-client mode with additional jar") {
     testWithAddJar(true)
   }
@@ -181,6 +186,15 @@ class YarnClusterSuite extends BaseYarnClusterSuite {
     checkResult(finalState, result)
   }
 
+  private def testYarnAppUseSparkHadoopUtilConf(): Unit = {
+    val result = File.createTempFile("result", null, tempDir)
+    val finalState = runSpark(false,
+      mainClassName(YarnClusterDriverUseSparkHadoopUtilConf.getClass),
+      appArgs = Seq("key=value", result.getAbsolutePath()),
+      extraConf = Map("spark.hadoop.key" -> "value"))
+    checkResult(finalState, result)
+  }
+
   private def testWithAddJar(clientMode: Boolean): Unit = {
     val originalJar = TestUtils.createJarWithFiles(Map("test.resource" -> "ORIGINAL"), tempDir)
     val driverResult = File.createTempFile("driver", null, tempDir)
@@ -274,6 +288,37 @@ private object YarnClusterDriverWithFailure extends Logging with Matchers {
   }
 }
 
+private object YarnClusterDriverUseSparkHadoopUtilConf extends Logging with Matchers {
+  def main(args: Array[String]): Unit = {
+    if (args.length != 2) {
+      // scalastyle:off println
+      System.err.println(
+        s"""
+        |Invalid command line: ${args.mkString(" ")}
+        |
+        |Usage: YarnClusterDriverUseSparkHadoopUtilConf [hadoopConfKey=value] [result file]
+        """.stripMargin)
+      // scalastyle:on println
+      System.exit(1)
+    }
+
+    val sc = new SparkContext(new SparkConf()
+      .set("spark.extraListeners", classOf[SaveExecutorInfo].getName)
+      .setAppName("yarn test using SparkHadoopUtil's conf"))
+
+    val kv = args(0).split("=")
+    val status = new File(args(1))
+    var result = "failure"
+    try {
+      SparkHadoopUtil.get.conf.get(kv(0)) should be (kv(1))
+      result = "success"
+    } finally {
+      Files.write(result, status, StandardCharsets.UTF_8)
+      sc.stop()
+    }
+  }
+}
+
 private object YarnClusterDriver extends Logging with Matchers {
 
   val WAIT_TIMEOUT_MILLIS = 10000