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HADOOP-2558 org.onelab.filter.BloomFilter class uses 8X the memory it should be using 

git-svn-id: https://svn.apache.org/repos/asf/lucene/hadoop/trunk/src/contrib/hbase@611734 13f79535-47bb-0310-9956-ffa450edef68
This commit is contained in:
Jim Kellerman 2008-01-14 08:09:11 +00:00
parent 27afba4ead
commit 728cb9c5df
6 changed files with 61 additions and 233 deletions
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2
CHANGES.txt
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@ -177,6 +177,8 @@ Trunk (unreleased changes)
HADOOP-2548 Make TableMap and TableReduce generic
(Frederik Hedberg via Stack)
HADOOP-2557 Shell count function (Edward Yoon via Stack)
HADOOP-2558 org.onelab.filter.BloomFilter class uses 8X the memory it should
be using
Release 0.15.1
Branch 0.15

123
src/java/org/onelab/filter/BloomFilter.java
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@ -51,6 +51,8 @@ import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.util.BitSet;
/**
* Implements a <i>Bloom filter</i>, as defined by Bloom in 1970.
* <p>
@ -72,11 +74,24 @@ import java.io.IOException;
* @see <a href="http://portal.acm.org/citation.cfm?id=362692&dl=ACM&coll=portal">Space/Time Trade-Offs in Hash Coding with Allowable Errors</a>
*/
public class BloomFilter extends Filter {
private static final byte[] bitvalues = new byte[] {
(byte)0x01,
(byte)0x02,
(byte)0x04,
(byte)0x08,
(byte)0x10,
(byte)0x20,
(byte)0x40,
(byte)0x80
};
/** The bit vector. */
boolean[] vector;
BitSet bits;
/** Default constructor - use with readFields */
public BloomFilter() {}
public BloomFilter() {
super();
}
/**
* Constructor
@ -86,7 +101,7 @@ public class BloomFilter extends Filter {
public BloomFilter(int vectorSize, int nbHash){
super(vectorSize, nbHash);
vector = new boolean[this.vectorSize];
bits = new BitSet(this.vectorSize);
}//end constructor
/** {@inheritDoc} */
@ -100,7 +115,7 @@ public class BloomFilter extends Filter {
hash.clear();
for(int i = 0; i < nbHash; i++) {
vector[h[i]] = true;
bits.set(h[i]);
}
}//end add()
@ -114,11 +129,7 @@ public class BloomFilter extends Filter {
throw new IllegalArgumentException("filters cannot be and-ed");
}
BloomFilter bf = (BloomFilter)filter;
for(int i = 0; i < vectorSize; i++) {
this.vector[i] &= bf.vector[i];
}
this.bits.and(((BloomFilter) filter).bits);
}//end and()
/** {@inheritDoc} */
@ -131,7 +142,7 @@ public class BloomFilter extends Filter {
int[] h = hash.hash(key);
hash.clear();
for(int i = 0; i < nbHash; i++) {
if(!vector[h[i]]) {
if(!bits.get(h[i])) {
return false;
}
}
@ -141,9 +152,7 @@ public class BloomFilter extends Filter {
/** {@inheritDoc} */
@Override
public void not(){
for(int i = 0; i < vectorSize; i++) {
vector[i] = !vector[i];
}
bits.flip(0, vectorSize - 1);
}//end not()
/** {@inheritDoc} */
@ -155,12 +164,7 @@ public class BloomFilter extends Filter {
|| filter.nbHash != this.nbHash) {
throw new IllegalArgumentException("filters cannot be or-ed");
}
BloomFilter bf = (BloomFilter)filter;
for(int i = 0; i < vectorSize; i++) {
this.vector[i] |= bf.vector[i];
}
bits.or(((BloomFilter) filter).bits);
}//end or()
/** {@inheritDoc} */
@ -172,24 +176,13 @@ public class BloomFilter extends Filter {
|| filter.nbHash != this.nbHash) {
throw new IllegalArgumentException("filters cannot be xor-ed");
}
BloomFilter bf = (BloomFilter)filter;
for(int i = 0; i < vectorSize; i++) {
this.vector[i] = (this.vector[i] && !bf.vector[i])
|| (!this.vector[i] && bf.vector[i]);
}
bits.xor(((BloomFilter) filter).bits);
}//and xor()
/** {@inheritDoc} */
@Override
public String toString(){
StringBuilder res = new StringBuilder();
for(int i = 0; i < vectorSize; i++) {
res.append(vector[i] ? "1" : "0");
}
return res.toString();
return bits.toString();
}//end toString()
/** {@inheritDoc} */
@ -200,56 +193,50 @@ public class BloomFilter extends Filter {
return bf;
}//end clone()
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
return this.compareTo(o) == 0;
}
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = super.hashCode();
for(int i = 0; i < vector.length; i++) {
result ^= Boolean.valueOf(vector[i]).hashCode();
}
return result;
}
// Writable
/** {@inheritDoc} */
@Override
public void write(DataOutput out) throws IOException {
super.write(out);
for(int i = 0; i < vector.length; i++) {
out.writeBoolean(vector[i]);
byte[] bytes = new byte[getNBytes()];
for(int i = 0, byteIndex = 0, bitIndex = 0; i < vectorSize; i++, bitIndex++) {
if (bitIndex == 8) {
bitIndex = 0;
byteIndex++;
}
if (bitIndex == 0) {
bytes[byteIndex] = 0;
}
if (bits.get(i)) {
bytes[byteIndex] |= bitvalues[bitIndex];
}
}
out.write(bytes);
}
/** {@inheritDoc} */
@Override
public void readFields(DataInput in) throws IOException {
super.readFields(in);
vector = new boolean[vectorSize];
for(int i = 0; i < vector.length; i++) {
vector[i] = in.readBoolean();
byte[] bytes = new byte[getNBytes()];
in.readFully(bytes);
for(int i = 0, byteIndex = 0, bitIndex = 0; i < vectorSize; i++, bitIndex++) {
if (bitIndex == 8) {
bitIndex = 0;
byteIndex++;
}
if (bitIndex == 0) {
bytes[byteIndex] = 0;
}
if ((bytes[byteIndex] & bitvalues[bitIndex]) != 0) {
bits.set(i);
}
}
}
// Comparable
/** {@inheritDoc} */
@Override
public int compareTo(Object o) {
int result = super.compareTo(o);
BloomFilter other = (BloomFilter)o;
for(int i = 0; result == 0 && i < vector.length; i++) {
result = (vector[i] == other.vector[i] ? 0
: (vector[i] ? 1 : -1));
}
return result;
}// end compareTo
/* @return number of bytes needed to hold bit vector */
private int getNBytes() {
return (vectorSize + 7) / 8;
}
}//end class

37
src/java/org/onelab/filter/CountingBloomFilter.java
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@ -213,22 +213,6 @@ public final class CountingBloomFilter extends Filter {
return cbf;
}//end clone()
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
return this.compareTo(o) == 0;
}
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = super.hashCode();
for(int i = 0; i < vector.length; i++) {
result ^= Byte.valueOf(vector[i]).hashCode();
}
return result;
}
// Writable
/** {@inheritDoc} */
@ -249,25 +233,4 @@ public final class CountingBloomFilter extends Filter {
vector[i] = in.readByte();
}
}
// Comparable
/** {@inheritDoc} */
@Override
public int compareTo(Object o) {
int result = super.compareTo(o);
if(result == 0) {
CountingBloomFilter other = (CountingBloomFilter)o;
for(int i = 0; i < vector.length; i++) {
result = vector[i] - other.vector[i];
if(result != 0) {
break;
}
}
}
return result;
}// end compareTo
}//end class

45
src/java/org/onelab/filter/DynamicBloomFilter.java
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@ -247,22 +247,6 @@ public class DynamicBloomFilter extends Filter {
return dbf;
}//end clone()
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
return this.compareTo(o) == 0;
}
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = super.hashCode();
for(int i = 0; i < matrix.length; i++) {
result ^= matrix[i].hashCode();
}
return result;
}
// Writable
/** {@inheritDoc} */
@ -284,35 +268,6 @@ public class DynamicBloomFilter extends Filter {
}
}
// Comparable
/** {@inheritDoc} */
@Override
public int compareTo(Object o) {
int result = super.compareTo(o);
if(result == 0) {
DynamicBloomFilter other = (DynamicBloomFilter)o;
result = this.nr - other.nr;
if(result == 0) {
result = this.currentNbRecord - other.currentNbRecord;
if(result == 0) {
for(int i = 0; i < matrix.length; i++) {
result = matrix[i].compareTo(other.matrix[i]) ;
if(result != 0) {
break;
}
}
}
}
}
return result;
}// end compareTo
/**
* Adds a new row to <i>this</i> dynamic Bloom filter.
*/

27
src/java/org/onelab/filter/Filter.java
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@ -54,7 +54,7 @@ import java.io.DataOutput;
import java.io.IOException;
import java.util.Collection;
import java.util.List;
import org.apache.hadoop.io.WritableComparable;
import org.apache.hadoop.io.Writable;
/**
* Defines the general behavior of a filter.
@ -74,7 +74,7 @@ import org.apache.hadoop.io.WritableComparable;
* @see org.onelab.filter.Key The general behavior of a key
* @see org.onelab.filter.HashFunction A hash function
*/
public abstract class Filter implements WritableComparable {
public abstract class Filter implements Writable {
/** The vector size of <i>this</i> filter. */
int vectorSize;
@ -182,14 +182,6 @@ public abstract class Filter implements WritableComparable {
}
}//end add()
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = Integer.valueOf(this.nbHash).hashCode();
result ^= Integer.valueOf(this.vectorSize);
return result;
}
// Writable interface
/** {@inheritDoc} */
@ -204,19 +196,4 @@ public abstract class Filter implements WritableComparable {
this.vectorSize = in.readInt();
this.hash = new HashFunction(this.vectorSize, this.nbHash);
}
// Comparable interface
/** {@inheritDoc} */
public int compareTo(Object o) {
Filter other = (Filter)o;
int result = this.vectorSize - other.vectorSize;
if(result == 0) {
result = this.nbHash - other.nbHash;
}
return result;
}
}//end class

60
src/java/org/onelab/filter/RetouchedBloomFilter.java
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@ -118,7 +118,7 @@ implements RemoveScheme {
hash.clear();
for(int i = 0; i < nbHash; i++) {
vector[h[i]] = true;
bits.set(h[i]);
keyVector[h[i]].add(key);
}//end for - i
}//end add()
@ -333,7 +333,7 @@ implements RemoveScheme {
ratio[index] = 0.0;
//update bit vector
vector[index] = false;
bits.clear(index);
}//end clearBit()
/**
@ -395,28 +395,6 @@ implements RemoveScheme {
}//end for -i
}//end createVector()
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
return this.compareTo(o) == 0;
}
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = super.hashCode();
for(int i = 0; i < fpVector.length; i++) {
result ^= fpVector[i].hashCode();
}
for(int i = 0; i < keyVector.length; i++) {
result ^= keyVector[i].hashCode();
}
for(int i = 0; i < ratio.length; i++) {
result ^= Double.valueOf(ratio[i]).hashCode();
}
return result;
}
// Writable
/** {@inheritDoc} */
@ -469,38 +447,4 @@ implements RemoveScheme {
ratio[i] = in.readDouble();
}
}
// Comparable
/** {@inheritDoc} */
@Override
public int compareTo(Object o) {
int result = super.compareTo(o);
RetouchedBloomFilter other = (RetouchedBloomFilter)o;
for(int i = 0; result == 0 && i < fpVector.length; i++) {
List<Key> mylist = fpVector[i];
List<Key> otherlist = other.fpVector[i];
for(int j = 0; result == 0 && j < mylist.size(); j++) {
result = mylist.get(j).compareTo(otherlist.get(j));
}
}
for(int i = 0; result == 0 && i < keyVector.length; i++) {
List<Key> mylist = keyVector[i];
List<Key> otherlist = other.keyVector[i];
for(int j = 0; result == 0 && j < mylist.size(); j++) {
result = mylist.get(j).compareTo(otherlist.get(j));
}
}
for(int i = 0; result == 0 && i < ratio.length; i++) {
result = Double.valueOf(this.ratio[i] - other.ratio[i]).intValue();
}
return result;
}// end compareTo
}//end class