[SPARK-14131][STREAMING] SQL Improved fix for avoiding potential deadlocks in HDFSMetadataLog

## What changes were proposed in this pull request?
Current fix for deadlock disables interrupts in the StreamExecution which getting offsets for all sources, and when writing to any metadata log, to avoid potential deadlocks in HDFSMetadataLog(see JIRA for more details). However, disabling interrupts can have unintended consequences in other sources. So I am making the fix more narrow, by disabling interrupt it only in the HDFSMetadataLog. This is a narrower fix for something risky like disabling interrupt.

## How was this patch tested?
Existing tests.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #14292 from tdas/SPARK-14131.

(cherry picked from commit c979c8b)
Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>

Author: tdas

sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLog.scala

@@ -32,6 +32,7 @@ import org.apache.spark.internal.Logging
 import org.apache.spark.network.util.JavaUtils
 import org.apache.spark.serializer.JavaSerializer
 import org.apache.spark.sql.SparkSession
+import org.apache.spark.util.UninterruptibleThread
 
 
 /**
@@ -91,18 +92,30 @@ class HDFSMetadataLog[T: ClassTag](sparkSession: SparkSession, path: String)
     serializer.deserialize[T](ByteBuffer.wrap(bytes))
   }
 
+  /**
+   * Store the metadata for the specified batchId and return `true` if successful. If the batchId's
+   * metadata has already been stored, this method will return `false`.
+   *
+   * Note that this method must be called on a [[org.apache.spark.util.UninterruptibleThread]]
+   * so that interrupts can be disabled while writing the batch file. This is because there is a
+   * potential dead-lock in Hadoop "Shell.runCommand" before 2.5.0 (HADOOP-10622). If the thread
+   * running "Shell.runCommand" is interrupted, then the thread can get deadlocked. In our
+   * case, `writeBatch` creates a file using HDFS API and calls "Shell.runCommand" to set the
+   * file permissions, and can get deadlocked if the stream execution thread is stopped by
+   * interrupt. Hence, we make sure that this method is called on [[UninterruptibleThread]] which
+   * allows us to disable interrupts here. Also see SPARK-14131.
+   */
   override def add(batchId: Long, metadata: T): Boolean = {
     get(batchId).map(_ => false).getOrElse {
-      // Only write metadata when the batch has not yet been written.
-      try {
-        writeBatch(batchId, serialize(metadata))
-        true
-      } catch {
-        case e: IOException if "java.lang.InterruptedException" == e.getMessage =>
-          // create may convert InterruptedException to IOException. Let's convert it back to
-          // InterruptedException so that this failure won't crash StreamExecution
-          throw new InterruptedException("Creating file is interrupted")
+      // Only write metadata when the batch has not yet been written
+      Thread.currentThread match {
+        case ut: UninterruptibleThread =>
+          ut.runUninterruptibly { writeBatch(batchId, serialize(metadata)) }
+        case _ =>
+          throw new IllegalStateException(
+            "HDFSMetadataLog.add() must be executed on a o.a.spark.util.UninterruptibleThread")
       }
+      true
     }
   }
 

sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/StreamExecution.scala

@@ -110,7 +110,11 @@ class StreamExecution(
   /* Get the call site in the caller thread; will pass this into the micro batch thread */
   private val callSite = Utils.getCallSite()
 
-  /** The thread that runs the micro-batches of this stream. */
+  /**
+   * The thread that runs the micro-batches of this stream. Note that this thread must be
+   * [[org.apache.spark.util.UninterruptibleThread]] to avoid potential deadlocks in using
+   * [[HDFSMetadataLog]]. See SPARK-14131 for more details.
+   */
   private[sql] val microBatchThread =
     new UninterruptibleThread(s"stream execution thread for $name") {
       override def run(): Unit = {
@@ -269,19 +273,11 @@ class StreamExecution(
    * batchId counter is incremented and a new log entry is written with the newest offsets.
    */
   private def constructNextBatch(): Unit = {
-    // There is a potential dead-lock in Hadoop "Shell.runCommand" before 2.5.0 (HADOOP-10622).
-    // If we interrupt some thread running Shell.runCommand, we may hit this issue.
-    // As "FileStreamSource.getOffset" will create a file using HDFS API and call "Shell.runCommand"
-    // to set the file permission, we should not interrupt "microBatchThread" when running this
-    // method. See SPARK-14131.
-    //
     // Check to see what new data is available.
     val hasNewData = {
       awaitBatchLock.lock()
       try {
-        val newData = microBatchThread.runUninterruptibly {
-          uniqueSources.flatMap(s => s.getOffset.map(o => s -> o))
-        }
+        val newData = uniqueSources.flatMap(s => s.getOffset.map(o => s -> o))
         availableOffsets ++= newData
 
         if (dataAvailable) {
@@ -295,16 +291,8 @@ class StreamExecution(
       }
     }
     if (hasNewData) {
-      // There is a potential dead-lock in Hadoop "Shell.runCommand" before 2.5.0 (HADOOP-10622).
-      // If we interrupt some thread running Shell.runCommand, we may hit this issue.
-      // As "offsetLog.add" will create a file using HDFS API and call "Shell.runCommand" to set
-      // the file permission, we should not interrupt "microBatchThread" when running this method.
-      // See SPARK-14131.
-      microBatchThread.runUninterruptibly {
-        assert(
-          offsetLog.add(currentBatchId, availableOffsets.toCompositeOffset(sources)),
-          s"Concurrent update to the log.  Multiple streaming jobs detected for $currentBatchId")
-      }
+      assert(offsetLog.add(currentBatchId, availableOffsets.toCompositeOffset(sources)),
+        s"Concurrent update to the log. Multiple streaming jobs detected for $currentBatchId")
       logInfo(s"Committed offsets for batch $currentBatchId.")
     } else {
       awaitBatchLock.lock()

sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/FileStreamSinkLogSuite.scala

@@ -190,7 +190,7 @@ class FileStreamSinkLogSuite extends SparkFunSuite with SharedSQLContext {
     }
   }
 
-  test("compact") {
+  testWithUninterruptibleThread("compact") {
     withSQLConf(SQLConf.FILE_SINK_LOG_COMPACT_INTERVAL.key -> "3") {
       withFileStreamSinkLog { sinkLog =>
         for (batchId <- 0 to 10) {
@@ -210,7 +210,7 @@ class FileStreamSinkLogSuite extends SparkFunSuite with SharedSQLContext {
     }
   }
 
-  test("delete expired file") {
+  testWithUninterruptibleThread("delete expired file") {
     // Set FILE_SINK_LOG_CLEANUP_DELAY to 0 so that we can detect the deleting behaviour
     // deterministically
     withSQLConf(

sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLogSuite.scala

@@ -33,6 +33,7 @@ import org.apache.spark.{SparkConf, SparkFunSuite}
 import org.apache.spark.sql.execution.streaming.FakeFileSystem._
 import org.apache.spark.sql.execution.streaming.HDFSMetadataLog.{FileContextManager, FileManager, FileSystemManager}
 import org.apache.spark.sql.test.SharedSQLContext
+import org.apache.spark.util.UninterruptibleThread
 
 class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
 
@@ -56,7 +57,7 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
     }
   }
 
-  test("HDFSMetadataLog: basic") {
+  testWithUninterruptibleThread("HDFSMetadataLog: basic") {
     withTempDir { temp =>
       val dir = new File(temp, "dir") // use non-existent directory to test whether log make the dir
       val metadataLog = new HDFSMetadataLog[String](spark, dir.getAbsolutePath)
@@ -81,7 +82,8 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
     }
   }
 
-  testQuietly("HDFSMetadataLog: fallback from FileContext to FileSystem") {
+  testWithUninterruptibleThread(
+    "HDFSMetadataLog: fallback from FileContext to FileSystem", quietly = true) {
     spark.conf.set(
       s"fs.$scheme.impl",
       classOf[FakeFileSystem].getName)
@@ -101,7 +103,7 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
     }
   }
 
-  test("HDFSMetadataLog: restart") {
+  testWithUninterruptibleThread("HDFSMetadataLog: restart") {
     withTempDir { temp =>
       val metadataLog = new HDFSMetadataLog[String](spark, temp.getAbsolutePath)
       assert(metadataLog.add(0, "batch0"))
@@ -124,7 +126,7 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
       val waiter = new Waiter
       val maxBatchId = 100
       for (id <- 0 until 10) {
-        new Thread() {
+        new UninterruptibleThread(s"HDFSMetadataLog: metadata directory collision - thread $id") {
           override def run(): Unit = waiter {
             val metadataLog =
               new HDFSMetadataLog[String](spark, temp.getAbsolutePath)

sql/core/src/test/scala/org/apache/spark/sql/test/SQLTestUtils.scala

@@ -22,6 +22,7 @@ import java.util.UUID
 
 import scala.language.implicitConversions
 import scala.util.Try
+import scala.util.control.NonFatal
 
 import org.apache.hadoop.conf.Configuration
 import org.scalatest.BeforeAndAfterAll
@@ -34,7 +35,7 @@ import org.apache.spark.sql.catalyst.FunctionIdentifier
 import org.apache.spark.sql.catalyst.plans.logical.LogicalPlan
 import org.apache.spark.sql.catalyst.util._
 import org.apache.spark.sql.execution.FilterExec
-import org.apache.spark.util.Utils
+import org.apache.spark.util.{UninterruptibleThread, Utils}
 
 /**
  * Helper trait that should be extended by all SQL test suites.
@@ -247,6 +248,46 @@ private[sql] trait SQLTestUtils
       }
     }
   }
+
+  /** Run a test on a separate [[UninterruptibleThread]]. */
+  protected def testWithUninterruptibleThread(name: String, quietly: Boolean = false)
+    (body: => Unit): Unit = {
+    val timeoutMillis = 10000
+    @transient var ex: Throwable = null
+
+    def runOnThread(): Unit = {
+      val thread = new UninterruptibleThread(s"Testing thread for test $name") {
+        override def run(): Unit = {
+          try {
+            body
+          } catch {
+            case NonFatal(e) =>
+              ex = e
+          }
+        }
+      }
+      thread.setDaemon(true)
+      thread.start()
+      thread.join(timeoutMillis)
+      if (thread.isAlive) {
+        thread.interrupt()
+        // If this interrupt does not work, then this thread is most likely running something that
+        // is not interruptible. There is not much point to wait for the thread to termniate, and
+        // we rather let the JVM terminate the thread on exit.
+        fail(
+          s"Test '$name' running on o.a.s.util.UninterruptibleThread timed out after" +
+            s" $timeoutMillis ms")
+      } else if (ex != null) {
+        throw ex
+      }
+    }
+
+    if (quietly) {
+      testQuietly(name) { runOnThread() }
+    } else {
+      test(name) { runOnThread() }
+    }
+  }
 }
 
 private[sql] object SQLTestUtils {