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LUCENE-7371: Better compression of values in Lucene60PointsFormat.

This commit is contained in:
Adrien Grand 2016-07-05 16:54:19 +02:00
parent e92a38af90
commit 866398bea6
6 changed files with 280 additions and 45 deletions
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3
lucene/CHANGES.txt
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@ -117,6 +117,9 @@ Optimizations
* LUCENE-7351: Doc id compression for points. (Adrien Grand)
* LUCENE-7351: Point values are now better compressed using run-length
encoding. (Adrien Grand)
Other
* LUCENE-4787: Fixed some highlighting javadocs. (Michael Dodsworth via Adrien

8
lucene/codecs/src/java/org/apache/lucene/codecs/simpletext/SimpleTextPointsWriter.java
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@ -20,6 +20,7 @@ package org.apache.lucene.codecs.simpletext;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.function.IntFunction;
import org.apache.lucene.codecs.PointsReader;
import org.apache.lucene.codecs.PointsWriter;
@ -161,12 +162,15 @@ class SimpleTextPointsWriter extends PointsWriter {
}
@Override
protected void writeLeafBlockPackedValue(IndexOutput out, int[] commonPrefixLengths, byte[] bytes, int bytesOffset) throws IOException {
protected void writeLeafBlockPackedValues(IndexOutput out, int[] commonPrefixLengths, int count, int sortedDim, IntFunction<BytesRef> packedValues) throws IOException {
for (int i = 0; i < count; ++i) {
BytesRef packedValue = packedValues.apply(i);
// NOTE: we don't do prefix coding, so we ignore commonPrefixLengths
write(out, BLOCK_VALUE);
write(out, new BytesRef(bytes, bytesOffset, packedBytesLength).toString());
write(out, packedValue.toString());
newline(out);
}
}
}) {
values.intersect(fieldInfo.name, new IntersectVisitor() {

65
lucene/core/src/java/org/apache/lucene/util/bkd/BKDReader.java
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@ -20,6 +20,7 @@ import java.io.IOException;
import java.util.Arrays;
import org.apache.lucene.codecs.CodecUtil;
import org.apache.lucene.index.CorruptIndexException;
import org.apache.lucene.index.PointValues.IntersectVisitor;
import org.apache.lucene.index.PointValues.Relation;
import org.apache.lucene.store.IndexInput;
@ -345,6 +346,63 @@ public class BKDReader implements Accountable {
protected void visitDocValues(int[] commonPrefixLengths, byte[] scratchPackedValue, IndexInput in, int[] docIDs, int count, IntersectVisitor visitor) throws IOException {
visitor.grow(count);
readCommonPrefixes(commonPrefixLengths, scratchPackedValue, in);
int compressedDim = version < BKDWriter.VERSION_COMPRESSED_VALUES
? -1
: readCompressedDim(in);
if (compressedDim == -1) {
visitRawDocValues(commonPrefixLengths, scratchPackedValue, in, docIDs, count, visitor);
} else {
visitCompressedDocValues(commonPrefixLengths, scratchPackedValue, in, docIDs, count, visitor, compressedDim);
}
}
// Just read suffixes for every dimension
private void visitRawDocValues(int[] commonPrefixLengths, byte[] scratchPackedValue, IndexInput in, int[] docIDs, int count, IntersectVisitor visitor) throws IOException {
for (int i = 0; i < count; ++i) {
for(int dim=0;dim<numDims;dim++) {
int prefix = commonPrefixLengths[dim];
in.readBytes(scratchPackedValue, dim*bytesPerDim + prefix, bytesPerDim - prefix);
}
visitor.visit(docIDs[i], scratchPackedValue);
}
}
private void visitCompressedDocValues(int[] commonPrefixLengths, byte[] scratchPackedValue, IndexInput in, int[] docIDs, int count, IntersectVisitor visitor, int compressedDim) throws IOException {
// the byte at `compressedByteOffset` is compressed using run-length compression,
// other suffix bytes are stored verbatim
final int compressedByteOffset = compressedDim * bytesPerDim + commonPrefixLengths[compressedDim];
commonPrefixLengths[compressedDim]++;
int i;
for (i = 0; i < count; ) {
scratchPackedValue[compressedByteOffset] = in.readByte();
final int runLen = Byte.toUnsignedInt(in.readByte());
for (int j = 0; j < runLen; ++j) {
for(int dim=0;dim<numDims;dim++) {
int prefix = commonPrefixLengths[dim];
in.readBytes(scratchPackedValue, dim*bytesPerDim + prefix, bytesPerDim - prefix);
}
visitor.visit(docIDs[i+j], scratchPackedValue);
}
i += runLen;
}
if (i != count) {
throw new CorruptIndexException("Sub blocks do not add up to the expected count: " + count + " != " + i, in);
}
}
private int readCompressedDim(IndexInput in) throws IOException {
int compressedDim = in.readByte();
if (compressedDim < -1 || compressedDim >= numDims) {
throw new CorruptIndexException("Got compressedDim="+compressedDim, in);
}
return compressedDim;
}
private void readCommonPrefixes(int[] commonPrefixLengths, byte[] scratchPackedValue, IndexInput in) throws IOException {
for(int dim=0;dim<numDims;dim++) {
int prefix = in.readVInt();
commonPrefixLengths[dim] = prefix;
@ -353,13 +411,6 @@ public class BKDReader implements Accountable {
}
//System.out.println("R: " + dim + " of " + numDims + " prefix=" + prefix);
}
for(int i=0;i<count;i++) {
for(int dim=0;dim<numDims;dim++) {
int prefix = commonPrefixLengths[dim];
in.readBytes(scratchPackedValue, dim*bytesPerDim + prefix, bytesPerDim - prefix);
}
visitor.visit(docIDs[i], scratchPackedValue);
}
}
private void intersect(IntersectState state,

173
lucene/core/src/java/org/apache/lucene/util/bkd/BKDWriter.java
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@ -22,9 +22,12 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import java.util.function.IntFunction;
import org.apache.lucene.codecs.CodecUtil;
import org.apache.lucene.index.MergeState;
import org.apache.lucene.index.PointValues.IntersectVisitor;
import org.apache.lucene.index.PointValues.Relation;
import org.apache.lucene.store.ChecksumIndexInput;
import org.apache.lucene.store.Directory;
import org.apache.lucene.store.IOContext;
@ -43,7 +46,6 @@ import org.apache.lucene.util.PriorityQueue;
import org.apache.lucene.util.StringHelper;
// TODO
// - the compression is somewhat stupid now (delta vInt for 1024 docIDs, no compression for the byte[] values even though they have high locality)
// - allow variable length byte[] (across docs and dims), but this is quite a bit more hairy
// - we could also index "auto-prefix terms" here, and use better compression, and maybe only use for the "fully contained" case so we'd
// only index docIDs
@ -60,7 +62,7 @@ import org.apache.lucene.util.StringHelper;
* the requested <code>maxPointsInLeafNode</code>. Values that fall exactly
* on a cell boundary may be in either cell.
*
* <p>The number of dimensions can be 1 to 255, but every byte[] value is fixed length.
* <p>The number of dimensions can be 1 to 8, but every byte[] value is fixed length.
*
* <p>
* See <a href="https://www.cs.duke.edu/~pankaj/publications/papers/bkd-sstd.pdf">this paper</a> for details.
@ -69,7 +71,7 @@ import org.apache.lucene.util.StringHelper;
* and then uses up to the specified {@code maxMBSortInHeap} heap space for writing.
*
* <p>
* <b>NOTE</b>: This can write at most Integer.MAX_VALUE * <code>maxPointsInLeafNode</code> total points, and
* <b>NOTE</b>: This can write at most Integer.MAX_VALUE * <code>maxPointsInLeafNode</code> total points.
*
* @lucene.experimental */
@ -78,7 +80,8 @@ public class BKDWriter implements Closeable {
public static final String CODEC_NAME = "BKD";
public static final int VERSION_START = 0;
public static final int VERSION_COMPRESSED_DOC_IDS = 1;
public static final int VERSION_CURRENT = VERSION_COMPRESSED_DOC_IDS;
public static final int VERSION_COMPRESSED_VALUES = 2;
public static final int VERSION_CURRENT = VERSION_COMPRESSED_VALUES;
/** How many bytes each docs takes in the fixed-width offline format */
private final int bytesPerDoc;
@ -312,6 +315,8 @@ public class BKDWriter implements Closeable {
/** Which leaf block we are up to */
private int blockID;
private final byte[] packedValues;
public MergeReader(BKDReader bkd, MergeState.DocMap docMap) throws IOException {
this.bkd = bkd;
state = new BKDReader.IntersectState(bkd.in.clone(),
@ -327,6 +332,7 @@ public class BKDWriter implements Closeable {
//System.out.println(" leaf fp=" + fp);
}
state.in.seek(minFP);
this.packedValues = new byte[bkd.maxPointsInLeafNode * bkd.packedBytesLength];
}
public boolean next() throws IOException {
@ -341,18 +347,33 @@ public class BKDWriter implements Closeable {
docsInBlock = bkd.readDocIDs(state.in, state.in.getFilePointer(), state.scratchDocIDs);
assert docsInBlock > 0;
docBlockUpto = 0;
for(int dim=0;dim<bkd.numDims;dim++) {
int prefix = state.in.readVInt();
state.commonPrefixLengths[dim] = prefix;
if (prefix > 0) {
state.in.readBytes(state.scratchPackedValue, dim*bkd.bytesPerDim, prefix);
bkd.visitDocValues(state.commonPrefixLengths, state.scratchPackedValue, state.in, state.scratchDocIDs, docsInBlock, new IntersectVisitor() {
int i = 0;
@Override
public void visit(int docID) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public void visit(int docID, byte[] packedValue) throws IOException {
assert docID == state.scratchDocIDs[i];
System.arraycopy(packedValue, 0, packedValues, i * bkd.packedBytesLength, bkd.packedBytesLength);
i++;
}
@Override
public Relation compare(byte[] minPackedValue, byte[] maxPackedValue) {
throw new UnsupportedOperationException();
}
});
blockID++;
}
int oldDocID = state.scratchDocIDs[docBlockUpto++];
final int index = docBlockUpto++;
int oldDocID = state.scratchDocIDs[index];
int mappedDocID;
if (docMap == null) {
@ -360,13 +381,11 @@ public class BKDWriter implements Closeable {
} else {
mappedDocID = docMap.get(oldDocID);
}
for(int dim=0;dim<bkd.numDims;dim++) {
int prefix = state.commonPrefixLengths[dim];
state.in.readBytes(state.scratchPackedValue, dim*bkd.bytesPerDim + prefix, bkd.bytesPerDim - prefix);
}
if (mappedDocID != -1) {
// Not deleted!
docID = mappedDocID;
System.arraycopy(packedValues, index * bkd.packedBytesLength, state.scratchPackedValue, 0, bkd.packedBytesLength);
return true;
}
}
@ -518,11 +537,22 @@ public class BKDWriter implements Closeable {
writeLeafBlockDocs(out, leafBlockDocIDs, 0, leafCount);
writeCommonPrefixes(out, commonPrefixLengths, firstPackedValue);
// Write the full values:
for (int i=0;i<leafCount;i++) {
writeLeafBlockPackedValue(out, commonPrefixLengths, leafBlockPackedValues[i], 0);
final IntFunction<BytesRef> packedValues = new IntFunction<BytesRef>() {
final BytesRef scratch = new BytesRef();
{
scratch.length = packedBytesLength;
scratch.offset = 0;
}
@Override
public BytesRef apply(int i) {
scratch.bytes = leafBlockPackedValues[i];
return scratch;
}
};
writeLeafBlockPackedValues(out, commonPrefixLengths, leafCount, 0, packedValues);
leafCount = 0;
}
}
@ -896,12 +926,56 @@ public class BKDWriter implements Closeable {
DocIdsWriter.writeDocIds(docIDs, start, count, out);
}
protected void writeLeafBlockPackedValue(IndexOutput out, int[] commonPrefixLengths, byte[] bytes, int offset) throws IOException {
protected void writeLeafBlockPackedValues(IndexOutput out, int[] commonPrefixLengths, int count, int sortedDim, IntFunction<BytesRef> packedValues) throws IOException {
int prefixLenSum = Arrays.stream(commonPrefixLengths).sum();
if (prefixLenSum == packedBytesLength) {
// all values in this block are equal
out.writeByte((byte) -1);
} else {
assert commonPrefixLengths[sortedDim] < bytesPerDim;
out.writeByte((byte) sortedDim);
int compressedByteOffset = sortedDim * bytesPerDim + commonPrefixLengths[sortedDim];
commonPrefixLengths[sortedDim]++;
for (int i = 0; i < count; ) {
// do run-length compression on the byte at compressedByteOffset
int runLen = runLen(packedValues, i, Math.min(i + 0xff, count), compressedByteOffset);
assert runLen <= 0xff;
BytesRef first = packedValues.apply(i);
byte prefixByte = first.bytes[first.offset + compressedByteOffset];
out.writeByte(prefixByte);
out.writeByte((byte) runLen);
writeLeafBlockPackedValuesRange(out, commonPrefixLengths, i, i + runLen, packedValues);
i += runLen;
assert i <= count;
}
}
}
private void writeLeafBlockPackedValuesRange(IndexOutput out, int[] commonPrefixLengths, int start, int end, IntFunction<BytesRef> packedValues) throws IOException {
for (int i = start; i < end; ++i) {
BytesRef ref = packedValues.apply(i);
assert ref.length == packedBytesLength;
for(int dim=0;dim<numDims;dim++) {
int prefix = commonPrefixLengths[dim];
out.writeBytes(bytes, offset+dim*bytesPerDim+prefix, bytesPerDim-prefix);
out.writeBytes(ref.bytes, ref.offset + dim*bytesPerDim + prefix, bytesPerDim-prefix);
}
}
}
private static int runLen(IntFunction<BytesRef> packedValues, int start, int end, int byteOffset) {
BytesRef first = packedValues.apply(start);
byte b = first.bytes[first.offset + byteOffset];
for (int i = start + 1; i < end; ++i) {
BytesRef ref = packedValues.apply(i);
byte b2 = ref.bytes[ref.offset + byteOffset];
assert Byte.toUnsignedInt(b2) >= Byte.toUnsignedInt(b);
if (b != b2) {
return i - start;
}
}
return end - start;
}
protected void writeCommonPrefixes(IndexOutput out, int[] commonPrefixes, byte[] packedValue) throws IOException {
for(int dim=0;dim<numDims;dim++) {
@ -1058,6 +1132,11 @@ public class BKDWriter implements Closeable {
if (nodeID >= leafNodeOffset) {
// Leaf node: write block
// We can write the block in any order so by default we write it sorted by the dimension that has the
// least number of unique bytes at commonPrefixLengths[dim], which makes compression more efficient
int sortedDim = 0;
int sortedDimCardinality = Integer.MAX_VALUE;
for (int dim=0;dim<numDims;dim++) {
if (slices[dim].writer instanceof HeapPointWriter == false) {
// Adversarial cases can cause this, e.g. very lopsided data, all equal points, such that we started
@ -1081,9 +1160,29 @@ public class BKDWriter implements Closeable {
break;
}
}
int prefix = commonPrefixLengths[dim];
if (prefix < bytesPerDim) {
int cardinality = 1;
byte previous = scratch1[offset + prefix];
for (long i = 1; i < source.count; ++i) {
heapSource.readPackedValue(Math.toIntExact(source.start + i), scratch2);
byte b = scratch2[offset + prefix];
assert Byte.toUnsignedInt(previous) <= Byte.toUnsignedInt(b);
if (b != previous) {
cardinality++;
previous = b;
}
}
assert cardinality <= 256;
if (cardinality < sortedDimCardinality) {
sortedDim = dim;
sortedDimCardinality = cardinality;
}
}
}
PathSlice source = slices[0];
PathSlice source = slices[sortedDim];
// We ensured that maxPointsSortInHeap was >= maxPointsInLeafNode, so we better be in heap at this point:
HeapPointWriter heapSource = (HeapPointWriter) source.writer;
@ -1105,16 +1204,22 @@ public class BKDWriter implements Closeable {
writeCommonPrefixes(out, commonPrefixLengths, scratch1);
// Write the full values:
byte[] lastPackedValue = new byte[bytesPerDim];
for (int i=0;i<count;i++) {
heapSource.getPackedValueSlice(Math.toIntExact(source.start + i), scratchBytesRef);
assert numDims != 1 || valueInOrder(i, lastPackedValue, scratchBytesRef.bytes, scratchBytesRef.offset);
IntFunction<BytesRef> packedValues = new IntFunction<BytesRef>() {
final BytesRef scratch = new BytesRef();
// Make sure this value does in fact fall within this leaf cell:
assert valueInBounds(scratchBytesRef, minPackedValue, maxPackedValue);
writeLeafBlockPackedValue(out, commonPrefixLengths, scratchBytesRef.bytes, scratchBytesRef.offset);
{
scratch.length = packedBytesLength;
}
@Override
public BytesRef apply(int i) {
heapSource.getPackedValueSlice(Math.toIntExact(source.start + i), scratch);
return scratch;
}
};
assert valuesInOrderAndBounds(count, minPackedValue, maxPackedValue, packedValues);
writeLeafBlockPackedValues(out, commonPrefixLengths, count, sortedDim, packedValues);
} else {
// Inner node: partition/recurse
@ -1215,6 +1320,20 @@ public class BKDWriter implements Closeable {
}
}
// only called from assert
private boolean valuesInOrderAndBounds(int count, byte[] minPackedValue, byte[] maxPackedValue, IntFunction<BytesRef> values) throws IOException {
byte[] lastPackedValue = new byte[bytesPerDim];
for (int i=0;i<count;i++) {
BytesRef packedValue = values.apply(i);
assert packedValue.length == packedBytesLength;
assert numDims != 1 || valueInOrder(i, lastPackedValue, packedValue.bytes, packedValue.offset);
// Make sure this value does in fact fall within this leaf cell:
assert valueInBounds(packedValue, minPackedValue, maxPackedValue);
}
return true;
}
// only called from assert
private boolean valueInOrder(long ord, byte[] lastPackedValue, byte[] packedValue, int packedValueOffset) {
if (ord > 0 && StringHelper.compare(bytesPerDim, lastPackedValue, 0, packedValue, packedValueOffset) > 0) {

29
lucene/core/src/test/org/apache/lucene/util/bkd/TestBKD.java
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@ -507,6 +507,35 @@ public class TestBKD extends LuceneTestCase {
verify(docValues, null, numDims, numBytesPerDim);
}
// this should trigger run-length compression with lengths that are greater than 255
public void testOneDimTwoValues() throws Exception {
int numBytesPerDim = TestUtil.nextInt(random(), 2, 30);
int numDims = TestUtil.nextInt(random(), 1, 5);
int numDocs = atLeast(1000);
int theDim = random().nextInt(numDims);
byte[] value1 = new byte[numBytesPerDim];
random().nextBytes(value1);
byte[] value2 = new byte[numBytesPerDim];
random().nextBytes(value2);
byte[][][] docValues = new byte[numDocs][][];
for(int docID=0;docID<numDocs;docID++) {
byte[][] values = new byte[numDims][];
for(int dim=0;dim<numDims;dim++) {
if (dim == theDim) {
values[dim] = random().nextBoolean() ? value1 : value2;
} else {
values[dim] = new byte[numBytesPerDim];
random().nextBytes(values[dim]);
}
}
docValues[docID] = values;
}
verify(docValues, null, numDims, numBytesPerDim);
}
public void testMultiValued() throws Exception {
int numBytesPerDim = TestUtil.nextInt(random(), 2, 30);
int numDims = TestUtil.nextInt(random(), 1, 5);

29
lucene/test-framework/src/java/org/apache/lucene/index/BasePointsFormatTestCase.java
View File

@ -327,6 +327,35 @@ public abstract class BasePointsFormatTestCase extends BaseIndexFileFormatTestCa
verify(docValues, null, numDims, numBytesPerDim);
}
// this should trigger run-length compression with lengths that are greater than 255
public void testOneDimTwoValues() throws Exception {
int numBytesPerDim = TestUtil.nextInt(random(), 2, PointValues.MAX_NUM_BYTES);
int numDims = TestUtil.nextInt(random(), 1, PointValues.MAX_DIMENSIONS);
int numDocs = atLeast(1000);
int theDim = random().nextInt(numDims);
byte[] value1 = new byte[numBytesPerDim];
random().nextBytes(value1);
byte[] value2 = new byte[numBytesPerDim];
random().nextBytes(value2);
byte[][][] docValues = new byte[numDocs][][];
for(int docID=0;docID<numDocs;docID++) {
byte[][] values = new byte[numDims][];
for(int dim=0;dim<numDims;dim++) {
if (dim == theDim) {
values[dim] = random().nextBoolean() ? value1 : value2;
} else {
values[dim] = new byte[numBytesPerDim];
random().nextBytes(values[dim]);
}
}
docValues[docID] = values;
}
verify(docValues, null, numDims, numBytesPerDim);
}
// Tests on N-dimensional points where each dimension is a BigInteger
public void testBigIntNDims() throws Exception {