[SPARK-2650][SQL] Try to partially fix SPARK-2650 by adjusting initial buffer...

[SPARK-2650][SQL] Try to partially fix SPARK-2650 by adjusting initial buffer size and reducing memory allocation

JIRA issue: [SPARK-2650](https://issues.apache.org/jira/browse/SPARK-2650)

Please refer to [comments](https://issues.apache.org/jira/browse/SPARK-2650?focusedCommentId=14084397&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-14084397) of SPARK-2650 for some other details.

This PR adjusts the initial in-memory columnar buffer size to 1MB, same as the default value of Shark's `shark.column.partitionSize.mb` property when running in local mode. Will add Shark style partition size estimation in another PR.

Also, before this PR, `NullableColumnBuilder` copies the whole buffer to add the null positions section, and then `CompressibleColumnBuilder` copies and compresses the buffer again, even if compression is disabled (`PassThrough` compression scheme is used to disable compression). In this PR the first buffer copy is eliminated to reduce memory consumption.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #1769 from liancheng/spark-2650 and squashes the following commits:

88a042e [Cheng Lian] Fixed method visibility and removed dead code
001f2e5 [Cheng Lian] Try fixing SPARK-2650 by adjusting initial buffer size and reducing memory allocation

sql/core/src/main/scala/org/apache/spark/sql/columnar/ColumnBuilder.scala

@@ -118,7 +118,7 @@ private[sql] class BinaryColumnBuilder extends ComplexColumnBuilder(BINARY)
 private[sql] class GenericColumnBuilder extends ComplexColumnBuilder(GENERIC)
 
 private[sql] object ColumnBuilder {
-  val DEFAULT_INITIAL_BUFFER_SIZE = 10 * 1024 * 104
+  val DEFAULT_INITIAL_BUFFER_SIZE = 1024 * 1024
 
   private[columnar] def ensureFreeSpace(orig: ByteBuffer, size: Int) = {
     if (orig.remaining >= size) {

sql/core/src/main/scala/org/apache/spark/sql/columnar/NullableColumnBuilder.scala

@@ -36,9 +36,9 @@ import org.apache.spark.sql.Row
  * }}}
  */
 private[sql] trait NullableColumnBuilder extends ColumnBuilder {
-  private var nulls: ByteBuffer = _
+  protected var nulls: ByteBuffer = _
+  protected var nullCount: Int = _
   private var pos: Int = _
-  private var nullCount: Int = _
 
   abstract override def initialize(initialSize: Int, columnName: String, useCompression: Boolean) {
     nulls = ByteBuffer.allocate(1024)
@@ -78,4 +78,9 @@ private[sql] trait NullableColumnBuilder extends ColumnBuilder {
     buffer.rewind()
     buffer
   }
+
+  protected def buildNonNulls(): ByteBuffer = {
+    nulls.limit(nulls.position()).rewind()
+    super.build()
+  }
 }

sql/core/src/main/scala/org/apache/spark/sql/columnar/compression/CompressibleColumnBuilder.scala

@@ -46,8 +46,6 @@ private[sql] trait CompressibleColumnBuilder[T <: NativeType]
 
   this: NativeColumnBuilder[T] with WithCompressionSchemes =>
 
-  import CompressionScheme._
-
   var compressionEncoders: Seq[Encoder[T]] = _
 
   abstract override def initialize(initialSize: Int, columnName: String, useCompression: Boolean) {
@@ -81,28 +79,32 @@ private[sql] trait CompressibleColumnBuilder[T <: NativeType]
     }
   }
 
-  abstract override def build() = {
-    val rawBuffer = super.build()
+  override def build() = {
+    val nonNullBuffer = buildNonNulls()
+    val typeId = nonNullBuffer.getInt()
     val encoder: Encoder[T] = {
       val candidate = compressionEncoders.minBy(_.compressionRatio)
       if (isWorthCompressing(candidate)) candidate else PassThrough.encoder
     }
 
-    val headerSize = columnHeaderSize(rawBuffer)
+    // Header = column type ID + null count + null positions
+    val headerSize = 4 + 4 + nulls.limit()
     val compressedSize = if (encoder.compressedSize == 0) {
-      rawBuffer.limit - headerSize
+      nonNullBuffer.remaining()
     } else {
       encoder.compressedSize
     }
 
-    // Reserves 4 bytes for compression scheme ID
     val compressedBuffer = ByteBuffer
+      // Reserves 4 bytes for compression scheme ID
       .allocate(headerSize + 4 + compressedSize)
       .order(ByteOrder.nativeOrder)
-
-    copyColumnHeader(rawBuffer, compressedBuffer)
+      // Write the header
+      .putInt(typeId)
+      .putInt(nullCount)
+      .put(nulls)
 
     logInfo(s"Compressor for [$columnName]: $encoder, ratio: ${encoder.compressionRatio}")
-    encoder.compress(rawBuffer, compressedBuffer, columnType)
+    encoder.compress(nonNullBuffer, compressedBuffer, columnType)
   }
 }

sql/core/src/main/scala/org/apache/spark/sql/columnar/compression/CompressionScheme.scala

@@ -67,22 +67,6 @@ private[sql] object CompressionScheme {
       s"Unrecognized compression scheme type ID: $typeId"))
   }
 
-  def copyColumnHeader(from: ByteBuffer, to: ByteBuffer) {
-    // Writes column type ID
-    to.putInt(from.getInt())
-
-    // Writes null count
-    val nullCount = from.getInt()
-    to.putInt(nullCount)
-
-    // Writes null positions
-    var i = 0
-    while (i < nullCount) {
-      to.putInt(from.getInt())
-      i += 1
-    }
-  }
-
   def columnHeaderSize(columnBuffer: ByteBuffer): Int = {
     val header = columnBuffer.duplicate().order(ByteOrder.nativeOrder)
     val nullCount = header.getInt(4)

sql/core/src/test/scala/org/apache/spark/sql/columnar/compression/TestCompressibleColumnBuilder.scala

@@ -42,4 +42,3 @@ object TestCompressibleColumnBuilder {
     builder
   }
 }
-