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From r...@apache.org
Subject spark git commit: [SPARK-12937][SQL] bloom filter serialization
Date Tue, 26 Jan 2016 08:53:08 GMT
Repository: spark
Updated Branches:
  refs/heads/master d54cfed5a -> 6743de3a9


[SPARK-12937][SQL] bloom filter serialization

This PR adds serialization support for BloomFilter.

A version number is added to version the serialized binary format.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10920 from cloud-fan/bloom-filter.


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/6743de3a
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/6743de3a
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/6743de3a

Branch: refs/heads/master
Commit: 6743de3a98e3f0d0e6064ca1872fa88c3aeaa143
Parents: d54cfed
Author: Wenchen Fan <wenchen@databricks.com>
Authored: Tue Jan 26 00:53:05 2016 -0800
Committer: Reynold Xin <rxin@databricks.com>
Committed: Tue Jan 26 00:53:05 2016 -0800

----------------------------------------------------------------------
 .../org/apache/spark/util/sketch/BitArray.java  | 46 ++++++++++++++-----
 .../apache/spark/util/sketch/BloomFilter.java   | 42 ++++++++++++++++-
 .../spark/util/sketch/BloomFilterImpl.java      | 48 +++++++++++++++++++-
 .../spark/util/sketch/CountMinSketch.java       | 25 ++++++----
 .../spark/util/sketch/CountMinSketchImpl.java   | 22 +--------
 .../spark/util/sketch/BloomFilterSuite.scala    | 20 ++++++++
 6 files changed, 159 insertions(+), 44 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/main/java/org/apache/spark/util/sketch/BitArray.java
----------------------------------------------------------------------
diff --git a/common/sketch/src/main/java/org/apache/spark/util/sketch/BitArray.java b/common/sketch/src/main/java/org/apache/spark/util/sketch/BitArray.java
index 1bc665a..2a0484e 100644
--- a/common/sketch/src/main/java/org/apache/spark/util/sketch/BitArray.java
+++ b/common/sketch/src/main/java/org/apache/spark/util/sketch/BitArray.java
@@ -17,6 +17,9 @@
 
 package org.apache.spark.util.sketch;
 
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
 import java.util.Arrays;
 
 public final class BitArray {
@@ -24,6 +27,9 @@ public final class BitArray {
   private long bitCount;
 
   static int numWords(long numBits) {
+    if (numBits <= 0) {
+      throw new IllegalArgumentException("numBits must be positive, but got " + numBits);
+    }
     long numWords = (long) Math.ceil(numBits / 64.0);
     if (numWords > Integer.MAX_VALUE) {
       throw new IllegalArgumentException("Can't allocate enough space for " + numBits + "
bits");
@@ -32,13 +38,14 @@ public final class BitArray {
   }
 
   BitArray(long numBits) {
-    if (numBits <= 0) {
-      throw new IllegalArgumentException("numBits must be positive");
-    }
-    this.data = new long[numWords(numBits)];
+    this(new long[numWords(numBits)]);
+  }
+
+  private BitArray(long[] data) {
+    this.data = data;
     long bitCount = 0;
-    for (long value : data) {
-      bitCount += Long.bitCount(value);
+    for (long word : data) {
+      bitCount += Long.bitCount(word);
     }
     this.bitCount = bitCount;
   }
@@ -78,13 +85,28 @@ public final class BitArray {
     this.bitCount = bitCount;
   }
 
-  @Override
-  public boolean equals(Object o) {
-    if (this == o) return true;
-    if (o == null || !(o instanceof BitArray)) return false;
+  void writeTo(DataOutputStream out) throws IOException {
+    out.writeInt(data.length);
+    for (long datum : data) {
+      out.writeLong(datum);
+    }
+  }
+
+  static BitArray readFrom(DataInputStream in) throws IOException {
+    int numWords = in.readInt();
+    long[] data = new long[numWords];
+    for (int i = 0; i < numWords; i++) {
+      data[i] = in.readLong();
+    }
+    return new BitArray(data);
+  }
 
-    BitArray bitArray = (BitArray) o;
-    return Arrays.equals(data, bitArray.data);
+  @Override
+  public boolean equals(Object other) {
+    if (this == other) return true;
+    if (other == null || !(other instanceof BitArray)) return false;
+    BitArray that = (BitArray) other;
+    return Arrays.equals(data, that.data);
   }
 
   @Override

http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilter.java
----------------------------------------------------------------------
diff --git a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilter.java b/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilter.java
index 38949c6..00378d5 100644
--- a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilter.java
+++ b/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilter.java
@@ -17,6 +17,10 @@
 
 package org.apache.spark.util.sketch;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
 /**
  * A Bloom filter is a space-efficient probabilistic data structure, that is used to test
whether
  * an element is a member of a set. It returns false when the element is definitely not in
the
@@ -39,6 +43,28 @@ package org.apache.spark.util.sketch;
  * The implementation is largely based on the {@code BloomFilter} class from guava.
  */
 public abstract class BloomFilter {
+
+  public enum Version {
+    /**
+     * {@code BloomFilter} binary format version 1 (all values written in big-endian order):
+     * - Version number, always 1 (32 bit)
+     * - Total number of words of the underlying bit array (32 bit)
+     * - The words/longs (numWords * 64 bit)
+     * - Number of hash functions (32 bit)
+     */
+    V1(1);
+
+    private final int versionNumber;
+
+    Version(int versionNumber) {
+      this.versionNumber = versionNumber;
+    }
+
+    int getVersionNumber() {
+      return versionNumber;
+    }
+  }
+
   /**
    * Returns the false positive probability, i.e. the probability that
    * {@linkplain #mightContain(Object)} will erroneously return {@code true} for an object
that
@@ -83,7 +109,7 @@ public abstract class BloomFilter {
    * bloom filters are appropriately sized to avoid saturating them.
    *
    * @param other The bloom filter to combine this bloom filter with. It is not mutated.
-   * @throws IllegalArgumentException if {@code isCompatible(that) == false}
+   * @throws IncompatibleMergeException if {@code isCompatible(other) == false}
    */
   public abstract BloomFilter mergeInPlace(BloomFilter other) throws IncompatibleMergeException;
 
@@ -94,6 +120,20 @@ public abstract class BloomFilter {
   public abstract boolean mightContain(Object item);
 
   /**
+   * Writes out this {@link BloomFilter} to an output stream in binary format.
+   * It is the caller's responsibility to close the stream.
+   */
+  public abstract void writeTo(OutputStream out) throws IOException;
+
+  /**
+   * Reads in a {@link BloomFilter} from an input stream.
+   * It is the caller's responsibility to close the stream.
+   */
+  public static BloomFilter readFrom(InputStream in) throws IOException {
+    return BloomFilterImpl.readFrom(in);
+  }
+
+  /**
    * Computes the optimal k (number of hashes per element inserted in Bloom filter), given
the
    * expected insertions and total number of bits in the Bloom filter.
    *

http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilterImpl.java
----------------------------------------------------------------------
diff --git a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilterImpl.java
b/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilterImpl.java
index bbd6cf7..1c08d07 100644
--- a/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilterImpl.java
+++ b/common/sketch/src/main/java/org/apache/spark/util/sketch/BloomFilterImpl.java
@@ -17,7 +17,7 @@
 
 package org.apache.spark.util.sketch;
 
-import java.io.UnsupportedEncodingException;
+import java.io.*;
 
 public class BloomFilterImpl extends BloomFilter {
 
@@ -25,8 +25,32 @@ public class BloomFilterImpl extends BloomFilter {
   private final BitArray bits;
 
   BloomFilterImpl(int numHashFunctions, long numBits) {
+    this(new BitArray(numBits), numHashFunctions);
+  }
+
+  private BloomFilterImpl(BitArray bits, int numHashFunctions) {
+    this.bits = bits;
     this.numHashFunctions = numHashFunctions;
-    this.bits = new BitArray(numBits);
+  }
+
+  @Override
+  public boolean equals(Object other) {
+    if (other == this) {
+      return true;
+    }
+
+    if (other == null || !(other instanceof BloomFilterImpl)) {
+      return false;
+    }
+
+    BloomFilterImpl that = (BloomFilterImpl) other;
+
+    return this.numHashFunctions == that.numHashFunctions && this.bits.equals(that.bits);
+  }
+
+  @Override
+  public int hashCode() {
+    return bits.hashCode() * 31 + numHashFunctions;
   }
 
   @Override
@@ -161,4 +185,24 @@ public class BloomFilterImpl extends BloomFilter {
     this.bits.putAll(that.bits);
     return this;
   }
+
+  @Override
+  public void writeTo(OutputStream out) throws IOException {
+    DataOutputStream dos = new DataOutputStream(out);
+
+    dos.writeInt(Version.V1.getVersionNumber());
+    bits.writeTo(dos);
+    dos.writeInt(numHashFunctions);
+  }
+
+  public static BloomFilterImpl readFrom(InputStream in) throws IOException {
+    DataInputStream dis = new DataInputStream(in);
+
+    int version = dis.readInt();
+    if (version != Version.V1.getVersionNumber()) {
+      throw new IOException("Unexpected Bloom filter version number (" + version + ")");
+    }
+
+    return new BloomFilterImpl(BitArray.readFrom(dis), dis.readInt());
+  }
 }

http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketch.java
----------------------------------------------------------------------
diff --git a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketch.java
b/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketch.java
index 9f4ff42..00c0b1b 100644
--- a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketch.java
+++ b/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketch.java
@@ -55,10 +55,21 @@ import java.io.OutputStream;
  * This implementation is largely based on the {@code CountMinSketch} class from stream-lib.
  */
 abstract public class CountMinSketch {
-  /**
-   * Version number of the serialized binary format.
-   */
+
   public enum Version {
+    /**
+     * {@code CountMinSketch} binary format version 1 (all values written in big-endian order):
+     * - Version number, always 1 (32 bit)
+     * - Total count of added items (64 bit)
+     * - Depth (32 bit)
+     * - Width (32 bit)
+     * - Hash functions (depth * 64 bit)
+     * - Count table
+     *   - Row 0 (width * 64 bit)
+     *   - Row 1 (width * 64 bit)
+     *   - ...
+     *   - Row depth - 1 (width * 64 bit)
+     */
     V1(1);
 
     private final int versionNumber;
@@ -67,13 +78,11 @@ abstract public class CountMinSketch {
       this.versionNumber = versionNumber;
     }
 
-    public int getVersionNumber() {
+    int getVersionNumber() {
       return versionNumber;
     }
   }
 
-  public abstract Version version();
-
   /**
    * Returns the relative error (or {@code eps}) of this {@link CountMinSketch}.
    */
@@ -128,13 +137,13 @@ abstract public class CountMinSketch {
 
   /**
    * Writes out this {@link CountMinSketch} to an output stream in binary format.
-   * It is the caller's responsibility to close the stream
+   * It is the caller's responsibility to close the stream.
    */
   public abstract void writeTo(OutputStream out) throws IOException;
 
   /**
    * Reads in a {@link CountMinSketch} from an input stream.
-   * It is the caller's responsibility to close the stream
+   * It is the caller's responsibility to close the stream.
    */
   public static CountMinSketch readFrom(InputStream in) throws IOException {
     return CountMinSketchImpl.readFrom(in);

http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketchImpl.java
----------------------------------------------------------------------
diff --git a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketchImpl.java
b/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketchImpl.java
index 0209446..d088096 100644
--- a/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketchImpl.java
+++ b/common/sketch/src/main/java/org/apache/spark/util/sketch/CountMinSketchImpl.java
@@ -26,21 +26,6 @@ import java.io.UnsupportedEncodingException;
 import java.util.Arrays;
 import java.util.Random;
 
-/*
- * Binary format of a serialized CountMinSketchImpl, version 1 (all values written in big-endian
- * order):
- *
- * - Version number, always 1 (32 bit)
- * - Total count of added items (64 bit)
- * - Depth (32 bit)
- * - Width (32 bit)
- * - Hash functions (depth * 64 bit)
- * - Count table
- *   - Row 0 (width * 64 bit)
- *   - Row 1 (width * 64 bit)
- *   - ...
- *   - Row depth - 1 (width * 64 bit)
- */
 class CountMinSketchImpl extends CountMinSketch {
   public static final long PRIME_MODULUS = (1L << 31) - 1;
 
@@ -112,11 +97,6 @@ class CountMinSketchImpl extends CountMinSketch {
     return hash;
   }
 
-  @Override
-  public Version version() {
-    return Version.V1;
-  }
-
   private void initTablesWith(int depth, int width, int seed) {
     this.table = new long[depth][width];
     this.hashA = new long[depth];
@@ -327,7 +307,7 @@ class CountMinSketchImpl extends CountMinSketch {
   public void writeTo(OutputStream out) throws IOException {
     DataOutputStream dos = new DataOutputStream(out);
 
-    dos.writeInt(version().getVersionNumber());
+    dos.writeInt(Version.V1.getVersionNumber());
 
     dos.writeLong(this.totalCount);
     dos.writeInt(this.depth);

http://git-wip-us.apache.org/repos/asf/spark/blob/6743de3a/common/sketch/src/test/scala/org/apache/spark/util/sketch/BloomFilterSuite.scala
----------------------------------------------------------------------
diff --git a/common/sketch/src/test/scala/org/apache/spark/util/sketch/BloomFilterSuite.scala
b/common/sketch/src/test/scala/org/apache/spark/util/sketch/BloomFilterSuite.scala
index d2de509..a0408d2 100644
--- a/common/sketch/src/test/scala/org/apache/spark/util/sketch/BloomFilterSuite.scala
+++ b/common/sketch/src/test/scala/org/apache/spark/util/sketch/BloomFilterSuite.scala
@@ -17,6 +17,8 @@
 
 package org.apache.spark.util.sketch
 
+import java.io.{ByteArrayInputStream, ByteArrayOutputStream}
+
 import scala.reflect.ClassTag
 import scala.util.Random
 
@@ -25,6 +27,20 @@ import org.scalatest.FunSuite // scalastyle:ignore funsuite
 class BloomFilterSuite extends FunSuite { // scalastyle:ignore funsuite
   private final val EPSILON = 0.01
 
+  // Serializes and deserializes a given `BloomFilter`, then checks whether the deserialized
+  // version is equivalent to the original one.
+  private def checkSerDe(filter: BloomFilter): Unit = {
+    val out = new ByteArrayOutputStream()
+    filter.writeTo(out)
+    out.close()
+
+    val in = new ByteArrayInputStream(out.toByteArray)
+    val deserialized = BloomFilter.readFrom(in)
+    in.close()
+
+    assert(filter == deserialized)
+  }
+
   def testAccuracy[T: ClassTag](typeName: String, numItems: Int)(itemGen: Random => T):
Unit = {
     test(s"accuracy - $typeName") {
       // use a fixed seed to make the test predictable.
@@ -51,6 +67,8 @@ class BloomFilterSuite extends FunSuite { // scalastyle:ignore funsuite
       // Also check the actual fpp is not significantly higher than we expected.
       val actualFpp = errorCount.toDouble / (numItems - numInsertion)
       assert(actualFpp - fpp < EPSILON)
+
+      checkSerDe(filter)
     }
   }
 
@@ -76,6 +94,8 @@ class BloomFilterSuite extends FunSuite { // scalastyle:ignore funsuite
 
       items1.foreach(i => assert(filter1.mightContain(i)))
       items2.foreach(i => assert(filter1.mightContain(i)))
+
+      checkSerDe(filter1)
     }
   }
 


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