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Posted to commits@geode.apache.org by ud...@apache.org on 2016/02/22 22:43:12 UTC
[024/100] [abbrv] [partial] incubator-geode git commit: Merge
remote-tracking branch 'origin/develop' into feature/GEODE-917
http://git-wip-us.apache.org/repos/asf/incubator-geode/blob/5beaaedc/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/Bits.java
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diff --cc geode-core/src/main/java/com/gemstone/gemfire/internal/hll/Bits.java
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+++ b/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/Bits.java
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++/*
++ * Copyright (C) 2011 Clearspring Technologies, Inc.
++ *
++ * Licensed under the Apache License, Version 2.0 (the "License");
++ * you may not use this file except in compliance with the License.
++ * You may obtain a copy of the License at
++ *
++ * http://www.apache.org/licenses/LICENSE-2.0
++ *
++ * Unless required by applicable law or agreed to in writing, software
++ * distributed under the License is distributed on an "AS IS" BASIS,
++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
++ * See the License for the specific language governing permissions and
++ * limitations under the License.
++ */
++package com.gemstone.gemfire.internal.hll;
++
++import java.io.ByteArrayInputStream;
++import java.io.DataInput;
++import java.io.DataInputStream;
++import java.io.IOException;
++
++public class Bits {
++
++ public static int[] getBits(byte[] mBytes) throws IOException {
++ int bitSize = mBytes.length / 4;
++ int[] bits = new int[bitSize];
++ DataInputStream dis = new DataInputStream(new ByteArrayInputStream(mBytes));
++ for (int i = 0; i < bitSize; i++) {
++ bits[i] = dis.readInt();
++ }
++ return bits;
++ }
++
++ /**
++ * This method might be better described as
++ * "byte array to int array" or "data input to int array"
++ */
++ public static int[] getBits(DataInput dataIn, int byteLength) throws IOException {
++ int bitSize = byteLength / 4;
++ int[] bits = new int[bitSize];
++ for (int i = 0; i < bitSize; i++) {
++ bits[i] = dataIn.readInt();
++ }
++ return bits;
++ }
++
++}
http://git-wip-us.apache.org/repos/asf/incubator-geode/blob/5beaaedc/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/CardinalityMergeException.java
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diff --cc geode-core/src/main/java/com/gemstone/gemfire/internal/hll/CardinalityMergeException.java
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--- /dev/null
+++ b/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/CardinalityMergeException.java
@@@ -1,0 -1,0 +1,26 @@@
++/*
++ * Copyright (C) 2011 Clearspring Technologies, Inc.
++ *
++ * Licensed under the Apache License, Version 2.0 (the "License");
++ * you may not use this file except in compliance with the License.
++ * You may obtain a copy of the License at
++ *
++ * http://www.apache.org/licenses/LICENSE-2.0
++ *
++ * Unless required by applicable law or agreed to in writing, software
++ * distributed under the License is distributed on an "AS IS" BASIS,
++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
++ * See the License for the specific language governing permissions and
++ * limitations under the License.
++ */
++package com.gemstone.gemfire.internal.hll;
++
++
++
++@SuppressWarnings("serial")
++public abstract class CardinalityMergeException extends Exception {
++
++ public CardinalityMergeException(String message) {
++ super(message);
++ }
++}
http://git-wip-us.apache.org/repos/asf/incubator-geode/blob/5beaaedc/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/HyperLogLog.java
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diff --cc geode-core/src/main/java/com/gemstone/gemfire/internal/hll/HyperLogLog.java
index 0000000,0000000..7e88198
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--- /dev/null
+++ b/geode-core/src/main/java/com/gemstone/gemfire/internal/hll/HyperLogLog.java
@@@ -1,0 -1,0 +1,345 @@@
++/*
++ * Copyright (C) 2012 Clearspring Technologies, Inc.
++ *
++ * Licensed under the Apache License, Version 2.0 (the "License");
++ * you may not use this file except in compliance with the License.
++ * You may obtain a copy of the License at
++ *
++ * http://www.apache.org/licenses/LICENSE-2.0
++ *
++ * Unless required by applicable law or agreed to in writing, software
++ * distributed under the License is distributed on an "AS IS" BASIS,
++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
++ * See the License for the specific language governing permissions and
++ * limitations under the License.
++ */
++package com.gemstone.gemfire.internal.hll;
++
++import com.gemstone.gemfire.internal.redis.executor.hll.HllExecutor;
++
++import java.io.ByteArrayInputStream;
++import java.io.ByteArrayOutputStream;
++import java.io.DataInput;
++import java.io.DataInputStream;
++import java.io.DataOutput;
++import java.io.DataOutputStream;
++import java.io.Externalizable;
++import java.io.IOException;
++import java.io.ObjectInput;
++import java.io.ObjectOutput;
++import java.io.Serializable;
++
++/**
++ * Java implementation of HyperLogLog (HLL) algorithm from this paper:
++ * <p/>
++ * http://algo.inria.fr/flajolet/Publications/FlFuGaMe07.pdf
++ * <p/>
++ * HLL is an improved version of LogLog that is capable of estimating
++ * the cardinality of a set with accuracy = 1.04/sqrt(m) where
++ * m = 2^b. So we can control accuracy vs space usage by increasing
++ * or decreasing b.
++ * <p/>
++ * The main benefit of using HLL over LL is that it only requires 64%
++ * of the space that LL does to get the same accuracy.
++ * <p/>
++ * This implementation implements a single counter. If a large (millions)
++ * number of counters are required you may want to refer to:
++ * <p/>
++ * http://dsiutils.dsi.unimi.it/
++ * <p/>
++ * It has a more complex implementation of HLL that supports multiple counters
++ * in a single object, drastically reducing the java overhead from creating
++ * a large number of objects.
++ * <p/>
++ * This implementation leveraged a javascript implementation that Yammer has
++ * been working on:
++ * <p/>
++ * https://github.com/yammer/probablyjs
++ * <p>
++ * Note that this implementation does not include the long range correction function
++ * defined in the original paper. Empirical evidence shows that the correction
++ * function causes more harm than good.
++ * </p>
++ * <p/>
++ * <p>
++ * Users have different motivations to use different types of hashing functions.
++ * Rather than try to keep up with all available hash functions and to remove
++ * the concern of causing future binary incompatibilities this class allows clients
++ * to offer the value in hashed int or long form. This way clients are free
++ * to change their hash function on their own time line. We recommend using Google's
++ * Guava Murmur3_128 implementation as it provides good performance and speed when
++ * high precision is required. In our tests the 32bit MurmurHash function included
++ * in this project is faster and produces better results than the 32 bit murmur3
++ * implementation google provides.
++ * </p>
++ */
++public class HyperLogLog implements ICardinality, Serializable {
++
++ private static final long serialVersionUID = -4661220245111112301L;
++ private final RegisterSet registerSet;
++ private final int log2m;
++ private final double alphaMM;
++
++
++ /**
++ * Create a new HyperLogLog instance using the specified standard deviation.
++ *
++ * @param rsd - the relative standard deviation for the counter.
++ * smaller values create counters that require more space.
++ */
++ public HyperLogLog(double rsd) {
++ this(log2m(rsd));
++ }
++
++ private static int log2m(double rsd) {
++ return (int) (Math.log((1.106 / rsd) * (1.106 / rsd)) / Math.log(2));
++ }
++
++ /**
++ * Create a new HyperLogLog instance. The log2m parameter defines the accuracy of
++ * the counter. The larger the log2m the better the accuracy.
++ * <p/>
++ * accuracy = 1.04/sqrt(2^log2m)
++ *
++ * @param log2m - the number of bits to use as the basis for the HLL instance
++ */
++ public HyperLogLog(int log2m) {
++ this(log2m, new RegisterSet(1 << log2m));
++ }
++
++ /**
++ * Creates a new HyperLogLog instance using the given registers. Used for unmarshalling a serialized
++ * instance and for merging multiple counters together.
++ *
++ * @param registerSet - the initial values for the register set
++ */
++ @Deprecated
++ public HyperLogLog(int log2m, RegisterSet registerSet) {
++ if (log2m < 0 || log2m > 30) {
++ throw new IllegalArgumentException("log2m argument is "
++ + log2m + " and is outside the range [0, 30]");
++ }
++ this.registerSet = registerSet;
++ this.log2m = log2m;
++ int m = 1 << this.log2m;
++
++ alphaMM = getAlphaMM(log2m, m);
++ }
++
++ @Override
++ public boolean offerHashed(long hashedValue) {
++ // j becomes the binary address determined by the first b log2m of x
++ // j will be between 0 and 2^log2m
++ final int j = (int) (hashedValue >>> (Long.SIZE - log2m));
++ final int r = Long.numberOfLeadingZeros((hashedValue << this.log2m) | (1 << (this.log2m - 1)) + 1) + 1;
++ return registerSet.updateIfGreater(j, r);
++ }
++
++ @Override
++ public boolean offerHashed(int hashedValue) {
++ // j becomes the binary address determined by the first b log2m of x
++ // j will be between 0 and 2^log2m
++ final int j = hashedValue >>> (Integer.SIZE - log2m);
++ final int r = Integer.numberOfLeadingZeros((hashedValue << this.log2m) | (1 << (this.log2m - 1)) + 1) + 1;
++ return registerSet.updateIfGreater(j, r);
++ }
++
++ @Override
++ public boolean offer(Object o) {
++ final int x = MurmurHash.hash(o);
++ return offerHashed(x);
++ }
++
++
++ @Override
++ public long cardinality() {
++ double registerSum = 0;
++ int count = registerSet.count;
++ double zeros = 0.0;
++ for (int j = 0; j < registerSet.count; j++) {
++ int val = registerSet.get(j);
++ registerSum += 1.0 / (1 << val);
++ if (val == 0) {
++ zeros++;
++ }
++ }
++
++ double estimate = alphaMM * (1 / registerSum);
++
++ if (estimate <= (5.0 / 2.0) * count) {
++ // Small Range Estimate
++ return Math.round(linearCounting(count, zeros));
++ } else {
++ return Math.round(estimate);
++ }
++ }
++
++ @Override
++ public int sizeof() {
++ return registerSet.size * 4;
++ }
++
++ @Override
++ public byte[] getBytes() throws IOException {
++ ByteArrayOutputStream baos = new ByteArrayOutputStream();
++ DataOutput dos = new DataOutputStream(baos);
++ writeBytes(dos);
++
++ return baos.toByteArray();
++ }
++
++ private void writeBytes(DataOutput serializedByteStream) throws IOException {
++ serializedByteStream.writeInt(log2m);
++ serializedByteStream.writeInt(registerSet.size * 4);
++ for (int x : registerSet.readOnlyBits()) {
++ serializedByteStream.writeInt(x);
++ }
++ }
++
++ /**
++ * Add all the elements of the other set to this set.
++ * <p/>
++ * This operation does not imply a loss of precision.
++ *
++ * @param other A compatible Hyperloglog instance (same log2m)
++ * @throws CardinalityMergeException if other is not compatible
++ */
++ public void addAll(HyperLogLog other) throws CardinalityMergeException {
++ if (this.sizeof() != other.sizeof()) {
++ throw new HyperLogLogMergeException("Cannot merge estimators of different sizes");
++ }
++
++ registerSet.merge(other.registerSet);
++ }
++
++ @Override
++ public ICardinality merge(ICardinality... estimators) throws CardinalityMergeException {
++ HyperLogLog merged = new HyperLogLog(HllExecutor.DEFAULT_HLL_STD_DEV);//new HyperLogLog(log2m, new RegisterSet(this.registerSet.count));
++ merged.addAll(this);
++
++ if (estimators == null) {
++ return merged;
++ }
++
++ for (ICardinality estimator : estimators) {
++ if (!(estimator instanceof HyperLogLog)) {
++ throw new HyperLogLogMergeException("Cannot merge estimators of different class");
++ }
++ HyperLogLog hll = (HyperLogLog) estimator;
++ merged.addAll(hll);
++ }
++
++ return merged;
++ }
++
++ private Object writeReplace() {
++ return new SerializationHolder(this);
++ }
++
++ /**
++ * This class exists to support Externalizable semantics for
++ * HyperLogLog objects without having to expose a public
++ * constructor, public write/read methods, or pretend final
++ * fields aren't final.
++ *
++ * In short, Externalizable allows you to skip some of the more
++ * verbose meta-data default Serializable gets you, but still
++ * includes the class name. In that sense, there is some cost
++ * to this holder object because it has a longer class name. I
++ * imagine people who care about optimizing for that have their
++ * own work-around for long class names in general, or just use
++ * a custom serialization framework. Therefore we make no attempt
++ * to optimize that here (eg. by raising this from an inner class
++ * and giving it an unhelpful name).
++ */
++ private static class SerializationHolder implements Externalizable {
++
++ HyperLogLog hyperLogLogHolder;
++
++ public SerializationHolder(HyperLogLog hyperLogLogHolder) {
++ this.hyperLogLogHolder = hyperLogLogHolder;
++ }
++
++ /**
++ * required for Externalizable
++ */
++ @SuppressWarnings("unused")
++ public SerializationHolder() {
++
++ }
++
++ @Override
++ public void writeExternal(ObjectOutput out) throws IOException {
++ hyperLogLogHolder.writeBytes(out);
++ }
++
++ @Override
++ public void readExternal(ObjectInput in) throws IOException, ClassNotFoundException {
++ hyperLogLogHolder = Builder.build(in);
++ }
++
++ private Object readResolve() {
++ return hyperLogLogHolder;
++ }
++ }
++
++ public static class Builder implements IBuilder<ICardinality>, Serializable {
++
++ private static final long serialVersionUID = -979314356097156719L;
++ private double rsd;
++
++ public Builder(double rsd) {
++ this.rsd = rsd;
++ }
++
++ @Override
++ public HyperLogLog build() {
++ return new HyperLogLog(rsd);
++ }
++
++ @Override
++ public int sizeof() {
++ int log2m = log2m(rsd);
++ int k = 1 << log2m;
++ return RegisterSet.getBits(k) * 4;
++ }
++
++ public static HyperLogLog build(byte[] bytes) throws IOException {
++ ByteArrayInputStream bais = new ByteArrayInputStream(bytes);
++ return build(new DataInputStream(bais));
++ }
++
++ public static HyperLogLog build(DataInput serializedByteStream) throws IOException {
++ int log2m = serializedByteStream.readInt();
++ int byteArraySize = serializedByteStream.readInt();
++ return new HyperLogLog(log2m,
++ new RegisterSet(1 << log2m, Bits.getBits(serializedByteStream, byteArraySize)));
++ }
++ }
++
++ @SuppressWarnings("serial")
++ protected static class HyperLogLogMergeException extends CardinalityMergeException {
++
++ public HyperLogLogMergeException(String message) {
++ super(message);
++ }
++ }
++
++ protected static double getAlphaMM(final int p, final int m) {
++ // See the paper.
++ switch (p) {
++ case 4:
++ return 0.673 * m * m;
++ case 5:
++ return 0.697 * m * m;
++ case 6:
++ return 0.709 * m * m;
++ default:
++ return (0.7213 / (1 + 1.079 / m)) * m * m;
++ }
++ }
++
++ protected static double linearCounting(int m, double V) {
++ return m * Math.log(m / V);
++ }
++}