Merge branch 'master' into sparkR-alias

R/pkg/R/generics.R

@@ -254,8 +254,10 @@ setGeneric("flatMapValues", function(X, FUN) { standardGeneric("flatMapValues")
 
 # @rdname intersection
 # @export
-setGeneric("intersection", function(x, other, numPartitions = 1) {
-  standardGeneric("intersection") })
+setGeneric("intersection",
+           function(x, other, numPartitions = 1) {
+             standardGeneric("intersection")
+           })
 
 # @rdname keys
 # @export
@@ -489,9 +491,7 @@ setGeneric("sample",
 #' @rdname sample
 #' @export
 setGeneric("sample_frac",
-           function(x, withReplacement, fraction, seed) {
-             standardGeneric("sample_frac")
-           })
+           function(x, withReplacement, fraction, seed) { standardGeneric("sample_frac") })
 
 #' @rdname saveAsParquetFile
 #' @export
@@ -553,8 +553,8 @@ setGeneric("withColumn", function(x, colName, col) { standardGeneric("withColumn
 
 #' @rdname withColumnRenamed
 #' @export
-setGeneric("withColumnRenamed", function(x, existingCol, newCol) {
-  standardGeneric("withColumnRenamed") })
+setGeneric("withColumnRenamed",
+           function(x, existingCol, newCol) { standardGeneric("withColumnRenamed") })
 
 
 ###################### Column Methods ##########################

R/pkg/R/pairRDD.R

@@ -202,8 +202,8 @@ setMethod("partitionBy",
 
             packageNamesArr <- serialize(.sparkREnv$.packages,
                                          connection = NULL)
-            broadcastArr <- lapply(ls(.broadcastNames), function(name) {
-                                   get(name, .broadcastNames) })
+            broadcastArr <- lapply(ls(.broadcastNames),
+                                   function(name) { get(name, .broadcastNames) })
             jrdd <- getJRDD(x)
 
             # We create a PairwiseRRDD that extends RDD[(Int, Array[Byte])],

R/pkg/R/sparkR.R

@@ -22,7 +22,8 @@
 connExists <- function(env) {
   tryCatch({
     exists(".sparkRCon", envir = env) && isOpen(env[[".sparkRCon"]])
-  }, error = function(err) {
+  },
+  error = function(err) {
     return(FALSE)
   })
 }
@@ -153,7 +154,8 @@ sparkR.init <- function(
   .sparkREnv$backendPort <- backendPort
   tryCatch({
     connectBackend("localhost", backendPort)
-  }, error = function(err) {
+  },
+  error = function(err) {
     stop("Failed to connect JVM\n")
   })
 
@@ -264,7 +266,8 @@ sparkRHive.init <- function(jsc = NULL) {
   ssc <- callJMethod(sc, "sc")
   hiveCtx <- tryCatch({
     newJObject("org.apache.spark.sql.hive.HiveContext", ssc)
-  }, error = function(err) {
+  },
+  error = function(err) {
     stop("Spark SQL is not built with Hive support")
   })
 

R/pkg/inst/tests/test_sparkSQL.R

@@ -115,7 +115,8 @@ test_that("create DataFrame from RDD", {
   df <- jsonFile(sqlContext, jsonPathNa)
   hiveCtx <- tryCatch({
     newJObject("org.apache.spark.sql.hive.test.TestHiveContext", ssc)
-  }, error = function(err) {
+  },
+  error = function(err) {
     skip("Hive is not build with SparkSQL, skipped")
   })
   sql(hiveCtx, "CREATE TABLE people (name string, age double, height float)")
@@ -609,7 +610,8 @@ test_that("write.df() as parquet file", {
 test_that("test HiveContext", {
   hiveCtx <- tryCatch({
     newJObject("org.apache.spark.sql.hive.test.TestHiveContext", ssc)
-  }, error = function(err) {
+  },
+  error = function(err) {
     skip("Hive is not build with SparkSQL, skipped")
   })
   df <- createExternalTable(hiveCtx, "json", jsonPath, "json")

R/run-tests.sh

@@ -23,7 +23,7 @@ FAILED=0
 LOGFILE=$FWDIR/unit-tests.out
 rm -f $LOGFILE
 
-SPARK_TESTING=1 $FWDIR/../bin/sparkR --driver-java-options "-Dlog4j.configuration=file:$FWDIR/log4j.properties" $FWDIR/pkg/tests/run-all.R 2>&1 | tee -a $LOGFILE
+SPARK_TESTING=1 $FWDIR/../bin/sparkR --conf spark.buffer.pageSize=4m --driver-java-options "-Dlog4j.configuration=file:$FWDIR/log4j.properties" $FWDIR/pkg/tests/run-all.R 2>&1 | tee -a $LOGFILE
 FAILED=$((PIPESTATUS[0]||$FAILED))
 
 if [[ $FAILED != 0 ]]; then

core/src/main/java/org/apache/spark/shuffle/unsafe/UnsafeShuffleExternalSorter.java

@@ -59,14 +59,14 @@ final class UnsafeShuffleExternalSorter {
 
   private final Logger logger = LoggerFactory.getLogger(UnsafeShuffleExternalSorter.class);
 
-  private static final int PAGE_SIZE = PackedRecordPointer.MAXIMUM_PAGE_SIZE_BYTES;
   @VisibleForTesting
   static final int DISK_WRITE_BUFFER_SIZE = 1024 * 1024;
-  @VisibleForTesting
-  static final int MAX_RECORD_SIZE = PAGE_SIZE - 4;
 
   private final int initialSize;
   private final int numPartitions;
+  private final int pageSizeBytes;
+  @VisibleForTesting
+  final int maxRecordSizeBytes;
   private final TaskMemoryManager memoryManager;
   private final ShuffleMemoryManager shuffleMemoryManager;
   private final BlockManager blockManager;
@@ -109,7 +109,10 @@ public UnsafeShuffleExternalSorter(
     this.numPartitions = numPartitions;
     // Use getSizeAsKb (not bytes) to maintain backwards compatibility if no units are provided
     this.fileBufferSizeBytes = (int) conf.getSizeAsKb("spark.shuffle.file.buffer", "32k") * 1024;
-
+    this.pageSizeBytes = (int) Math.min(
+      PackedRecordPointer.MAXIMUM_PAGE_SIZE_BYTES,
+      conf.getSizeAsBytes("spark.buffer.pageSize", "64m"));
+    this.maxRecordSizeBytes = pageSizeBytes - 4;
     this.writeMetrics = writeMetrics;
     initializeForWriting();
   }
@@ -272,7 +275,11 @@ void spill() throws IOException {
   }
 
   private long getMemoryUsage() {
-    return sorter.getMemoryUsage() + (allocatedPages.size() * (long) PAGE_SIZE);
+    long totalPageSize = 0;
+    for (MemoryBlock page : allocatedPages) {
+      totalPageSize += page.size();
+    }
+    return sorter.getMemoryUsage() + totalPageSize;
   }
 
   private long freeMemory() {
@@ -346,23 +353,23 @@ private void allocateSpaceForRecord(int requiredSpace) throws IOException {
       // TODO: we should track metrics on the amount of space wasted when we roll over to a new page
       // without using the free space at the end of the current page. We should also do this for
       // BytesToBytesMap.
-      if (requiredSpace > PAGE_SIZE) {
+      if (requiredSpace > pageSizeBytes) {
         throw new IOException("Required space " + requiredSpace + " is greater than page size (" +
-          PAGE_SIZE + ")");
+          pageSizeBytes + ")");
       } else {
-        final long memoryAcquired = shuffleMemoryManager.tryToAcquire(PAGE_SIZE);
-        if (memoryAcquired < PAGE_SIZE) {
+        final long memoryAcquired = shuffleMemoryManager.tryToAcquire(pageSizeBytes);
+        if (memoryAcquired < pageSizeBytes) {
           shuffleMemoryManager.release(memoryAcquired);
           spill();
-          final long memoryAcquiredAfterSpilling = shuffleMemoryManager.tryToAcquire(PAGE_SIZE);
-          if (memoryAcquiredAfterSpilling != PAGE_SIZE) {
+          final long memoryAcquiredAfterSpilling = shuffleMemoryManager.tryToAcquire(pageSizeBytes);
+          if (memoryAcquiredAfterSpilling != pageSizeBytes) {
             shuffleMemoryManager.release(memoryAcquiredAfterSpilling);
-            throw new IOException("Unable to acquire " + PAGE_SIZE + " bytes of memory");
+            throw new IOException("Unable to acquire " + pageSizeBytes + " bytes of memory");
           }
         }
-        currentPage = memoryManager.allocatePage(PAGE_SIZE);
+        currentPage = memoryManager.allocatePage(pageSizeBytes);
         currentPagePosition = currentPage.getBaseOffset();
-        freeSpaceInCurrentPage = PAGE_SIZE;
+        freeSpaceInCurrentPage = pageSizeBytes;
         allocatedPages.add(currentPage);
       }
     }

core/src/main/java/org/apache/spark/shuffle/unsafe/UnsafeShuffleWriter.java

@@ -129,6 +129,11 @@ public UnsafeShuffleWriter(
     open();
   }
 
+  @VisibleForTesting
+  public int maxRecordSizeBytes() {
+    return sorter.maxRecordSizeBytes;
+  }
+
   /**
    * This convenience method should only be called in test code.
    */

core/src/main/java/org/apache/spark/util/collection/unsafe/sort/PrefixComparators.java

@@ -17,9 +17,7 @@
 
 package org.apache.spark.util.collection.unsafe.sort;
 
-import com.google.common.base.Charsets;
-import com.google.common.primitives.Longs;
-import com.google.common.primitives.UnsignedBytes;
+import com.google.common.primitives.UnsignedLongs;
 
 import org.apache.spark.annotation.Private;
 import org.apache.spark.unsafe.types.UTF8String;
@@ -37,32 +35,11 @@ private PrefixComparators() {}
   public static final class StringPrefixComparator extends PrefixComparator {
     @Override
     public int compare(long aPrefix, long bPrefix) {
-      // TODO: can done more efficiently
-      byte[] a = Longs.toByteArray(aPrefix);
-      byte[] b = Longs.toByteArray(bPrefix);
-      for (int i = 0; i < 8; i++) {
-        int c = UnsignedBytes.compare(a[i], b[i]);
-        if (c != 0) return c;
-      }
-      return 0;
-    }
-
-    public long computePrefix(byte[] bytes) {
-      if (bytes == null) {
-        return 0L;
-      } else {
-        byte[] padded = new byte[8];
-        System.arraycopy(bytes, 0, padded, 0, Math.min(bytes.length, 8));
-        return Longs.fromByteArray(padded);
-      }
-    }
-
-    public long computePrefix(String value) {
-      return value == null ? 0L : computePrefix(value.getBytes(Charsets.UTF_8));
+      return UnsignedLongs.compare(aPrefix, bPrefix);
     }
 
     public long computePrefix(UTF8String value) {
-      return value == null ? 0L : computePrefix(value.getBytes());
+      return value == null ? 0L : value.getPrefix();
     }
   }
 

core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java

@@ -20,6 +20,9 @@
 import java.io.IOException;
 import java.util.LinkedList;
 
+import scala.runtime.AbstractFunction0;
+import scala.runtime.BoxedUnit;
+
 import com.google.common.annotations.VisibleForTesting;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -41,10 +44,7 @@ public final class UnsafeExternalSorter {
 
   private final Logger logger = LoggerFactory.getLogger(UnsafeExternalSorter.class);
 
-  private static final int PAGE_SIZE = 1 << 27;  // 128 megabytes
-  @VisibleForTesting
-  static final int MAX_RECORD_SIZE = PAGE_SIZE - 4;
-
+  private final long pageSizeBytes;
   private final PrefixComparator prefixComparator;
   private final RecordComparator recordComparator;
   private final int initialSize;
@@ -91,7 +91,19 @@ public UnsafeExternalSorter(
     this.initialSize = initialSize;
     // Use getSizeAsKb (not bytes) to maintain backwards compatibility for units
     this.fileBufferSizeBytes = (int) conf.getSizeAsKb("spark.shuffle.file.buffer", "32k") * 1024;
+    this.pageSizeBytes = conf.getSizeAsBytes("spark.buffer.pageSize", "64m");
     initializeForWriting();
+
+    // Register a cleanup task with TaskContext to ensure that memory is guaranteed to be freed at
+    // the end of the task. This is necessary to avoid memory leaks in when the downstream operator
+    // does not fully consume the sorter's output (e.g. sort followed by limit).
+    taskContext.addOnCompleteCallback(new AbstractFunction0<BoxedUnit>() {
+      @Override
+      public BoxedUnit apply() {
+        freeMemory();
+        return null;
+      }
+    });
   }
 
   // TODO: metrics tracking + integration with shuffle write metrics
@@ -147,7 +159,11 @@ public void spill() throws IOException {
   }
 
   private long getMemoryUsage() {
-    return sorter.getMemoryUsage() + (allocatedPages.size() * (long) PAGE_SIZE);
+    long totalPageSize = 0;
+    for (MemoryBlock page : allocatedPages) {
+      totalPageSize += page.size();
+    }
+    return sorter.getMemoryUsage() + totalPageSize;
   }
 
   @VisibleForTesting
@@ -214,23 +230,23 @@ private void allocateSpaceForRecord(int requiredSpace) throws IOException {
       // TODO: we should track metrics on the amount of space wasted when we roll over to a new page
       // without using the free space at the end of the current page. We should also do this for
       // BytesToBytesMap.
-      if (requiredSpace > PAGE_SIZE) {
+      if (requiredSpace > pageSizeBytes) {
         throw new IOException("Required space " + requiredSpace + " is greater than page size (" +
-          PAGE_SIZE + ")");
+          pageSizeBytes + ")");
       } else {
-        final long memoryAcquired = shuffleMemoryManager.tryToAcquire(PAGE_SIZE);
-        if (memoryAcquired < PAGE_SIZE) {
+        final long memoryAcquired = shuffleMemoryManager.tryToAcquire(pageSizeBytes);
+        if (memoryAcquired < pageSizeBytes) {
           shuffleMemoryManager.release(memoryAcquired);
           spill();
-          final long memoryAcquiredAfterSpilling = shuffleMemoryManager.tryToAcquire(PAGE_SIZE);
-          if (memoryAcquiredAfterSpilling != PAGE_SIZE) {
+          final long memoryAcquiredAfterSpilling = shuffleMemoryManager.tryToAcquire(pageSizeBytes);
+          if (memoryAcquiredAfterSpilling != pageSizeBytes) {
             shuffleMemoryManager.release(memoryAcquiredAfterSpilling);
-            throw new IOException("Unable to acquire " + PAGE_SIZE + " bytes of memory");
+            throw new IOException("Unable to acquire " + pageSizeBytes + " bytes of memory");
           }
         }
-        currentPage = memoryManager.allocatePage(PAGE_SIZE);
+        currentPage = memoryManager.allocatePage(pageSizeBytes);
         currentPagePosition = currentPage.getBaseOffset();
-        freeSpaceInCurrentPage = PAGE_SIZE;
+        freeSpaceInCurrentPage = pageSizeBytes;
         allocatedPages.add(currentPage);
       }
     }

core/src/main/scala/org/apache/spark/Accumulators.scala

@@ -341,7 +341,4 @@ private[spark] object Accumulators extends Logging {
     }
   }
 
-  def stringifyPartialValue(partialValue: Any): String = "%s".format(partialValue)
-
-  def stringifyValue(value: Any): String = "%s".format(value)
 }