MAPREDUCE-5656. bzip2 codec can drop records when reading data in splits. Contributed by Jason Lowe

git-svn-id: https://svn.apache.org/repos/asf/hadoop/common/trunk@1549705 13f79535-47bb-0310-9956-ffa450edef68
This commit is contained in:
Jason Darrell Lowe 2013-12-09 23:31:30 +00:00
parent 87a6db45b7
commit 18d99c12c3
10 changed files with 442 additions and 31 deletions

View File

@ -175,6 +175,11 @@ public class LineReader implements Closeable {
} }
} }
protected int fillBuffer(InputStream in, byte[] buffer, boolean inDelimiter)
throws IOException {
return in.read(buffer);
}
/** /**
* Read a line terminated by one of CR, LF, or CRLF. * Read a line terminated by one of CR, LF, or CRLF.
*/ */
@ -208,7 +213,7 @@ public class LineReader implements Closeable {
if (prevCharCR) { if (prevCharCR) {
++bytesConsumed; //account for CR from previous read ++bytesConsumed; //account for CR from previous read
} }
bufferLength = in.read(buffer); bufferLength = fillBuffer(in, buffer, prevCharCR);
if (bufferLength <= 0) { if (bufferLength <= 0) {
break; // EOF break; // EOF
} }
@ -296,7 +301,7 @@ public class LineReader implements Closeable {
int startPosn = bufferPosn; // Start from previous end position int startPosn = bufferPosn; // Start from previous end position
if (bufferPosn >= bufferLength) { if (bufferPosn >= bufferLength) {
startPosn = bufferPosn = 0; startPosn = bufferPosn = 0;
bufferLength = in.read(buffer); bufferLength = fillBuffer(in, buffer, ambiguousByteCount > 0);
if (bufferLength <= 0) { if (bufferLength <= 0) {
str.append(recordDelimiterBytes, 0, ambiguousByteCount); str.append(recordDelimiterBytes, 0, ambiguousByteCount);
break; // EOF break; // EOF

View File

@ -231,6 +231,9 @@ Release 2.4.0 - UNRELEASED
MAPREDUCE-5632. TestRMContainerAllocator#testUpdatedNodes fails (jeagles) MAPREDUCE-5632. TestRMContainerAllocator#testUpdatedNodes fails (jeagles)
MAPREDUCE-5656. bzip2 codec can drop records when reading data in splits
(jlowe)
Release 2.3.0 - UNRELEASED Release 2.3.0 - UNRELEASED
INCOMPATIBLE CHANGES INCOMPATIBLE CHANGES

View File

@ -36,6 +36,8 @@ import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.hadoop.io.compress.Decompressor; import org.apache.hadoop.io.compress.Decompressor;
import org.apache.hadoop.io.compress.SplitCompressionInputStream; import org.apache.hadoop.io.compress.SplitCompressionInputStream;
import org.apache.hadoop.io.compress.SplittableCompressionCodec; import org.apache.hadoop.io.compress.SplittableCompressionCodec;
import org.apache.hadoop.mapreduce.lib.input.CompressedSplitLineReader;
import org.apache.hadoop.mapreduce.lib.input.SplitLineReader;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
@ -52,7 +54,7 @@ public class LineRecordReader implements RecordReader<LongWritable, Text> {
private long start; private long start;
private long pos; private long pos;
private long end; private long end;
private LineReader in; private SplitLineReader in;
private FSDataInputStream fileIn; private FSDataInputStream fileIn;
private final Seekable filePosition; private final Seekable filePosition;
int maxLineLength; int maxLineLength;
@ -111,17 +113,18 @@ public class LineRecordReader implements RecordReader<LongWritable, Text> {
((SplittableCompressionCodec)codec).createInputStream( ((SplittableCompressionCodec)codec).createInputStream(
fileIn, decompressor, start, end, fileIn, decompressor, start, end,
SplittableCompressionCodec.READ_MODE.BYBLOCK); SplittableCompressionCodec.READ_MODE.BYBLOCK);
in = new LineReader(cIn, job, recordDelimiter); in = new CompressedSplitLineReader(cIn, job, recordDelimiter);
start = cIn.getAdjustedStart(); start = cIn.getAdjustedStart();
end = cIn.getAdjustedEnd(); end = cIn.getAdjustedEnd();
filePosition = cIn; // take pos from compressed stream filePosition = cIn; // take pos from compressed stream
} else { } else {
in = new LineReader(codec.createInputStream(fileIn, decompressor), job, recordDelimiter); in = new SplitLineReader(codec.createInputStream(fileIn,
decompressor), job, recordDelimiter);
filePosition = fileIn; filePosition = fileIn;
} }
} else { } else {
fileIn.seek(start); fileIn.seek(start);
in = new LineReader(fileIn, job, recordDelimiter); in = new SplitLineReader(fileIn, job, recordDelimiter);
filePosition = fileIn; filePosition = fileIn;
} }
// If this is not the first split, we always throw away first record // If this is not the first split, we always throw away first record
@ -141,7 +144,7 @@ public class LineRecordReader implements RecordReader<LongWritable, Text> {
public LineRecordReader(InputStream in, long offset, long endOffset, public LineRecordReader(InputStream in, long offset, long endOffset,
int maxLineLength, byte[] recordDelimiter) { int maxLineLength, byte[] recordDelimiter) {
this.maxLineLength = maxLineLength; this.maxLineLength = maxLineLength;
this.in = new LineReader(in, recordDelimiter); this.in = new SplitLineReader(in, recordDelimiter);
this.start = offset; this.start = offset;
this.pos = offset; this.pos = offset;
this.end = endOffset; this.end = endOffset;
@ -159,7 +162,7 @@ public class LineRecordReader implements RecordReader<LongWritable, Text> {
throws IOException{ throws IOException{
this.maxLineLength = job.getInt(org.apache.hadoop.mapreduce.lib.input. this.maxLineLength = job.getInt(org.apache.hadoop.mapreduce.lib.input.
LineRecordReader.MAX_LINE_LENGTH, Integer.MAX_VALUE); LineRecordReader.MAX_LINE_LENGTH, Integer.MAX_VALUE);
this.in = new LineReader(in, job, recordDelimiter); this.in = new SplitLineReader(in, job, recordDelimiter);
this.start = offset; this.start = offset;
this.pos = offset; this.pos = offset;
this.end = endOffset; this.end = endOffset;
@ -200,7 +203,7 @@ public class LineRecordReader implements RecordReader<LongWritable, Text> {
// We always read one extra line, which lies outside the upper // We always read one extra line, which lies outside the upper
// split limit i.e. (end - 1) // split limit i.e. (end - 1)
while (getFilePosition() <= end) { while (getFilePosition() <= end || in.needAdditionalRecordAfterSplit()) {
key.set(pos); key.set(pos);
int newSize = in.readLine(value, maxLineLength, int newSize = in.readLine(value, maxLineLength,

View File

@ -0,0 +1,168 @@
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you 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 org.apache.hadoop.mapreduce.lib.input;
import java.io.IOException;
import java.io.InputStream;
import org.apache.hadoop.classification.InterfaceAudience;
import org.apache.hadoop.classification.InterfaceStability;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.SplitCompressionInputStream;
/**
* Line reader for compressed splits
*
* Reading records from a compressed split is tricky, as the
* LineRecordReader is using the reported compressed input stream
* position directly to determine when a split has ended. In addition the
* compressed input stream is usually faking the actual byte position, often
* updating it only after the first compressed block after the split is
* accessed.
*
* Depending upon where the last compressed block of the split ends relative
* to the record delimiters it can be easy to accidentally drop the last
* record or duplicate the last record between this split and the next.
*
* Split end scenarios:
*
* 1) Last block of split ends in the middle of a record
* Nothing special that needs to be done here, since the compressed input
* stream will report a position after the split end once the record
* is fully read. The consumer of the next split will discard the
* partial record at the start of the split normally, and no data is lost
* or duplicated between the splits.
*
* 2) Last block of split ends in the middle of a delimiter
* The line reader will continue to consume bytes into the next block to
* locate the end of the delimiter. If a custom delimiter is being used
* then the next record must be read by this split or it will be dropped.
* The consumer of the next split will not recognize the partial
* delimiter at the beginning of its split and will discard it along with
* the next record.
*
* However for the default delimiter processing there is a special case
* because CR, LF, and CRLF are all valid record delimiters. If the
* block ends with a CR then the reader must peek at the next byte to see
* if it is an LF and therefore part of the same record delimiter.
* Peeking at the next byte is an access to the next block and triggers
* the stream to report the end of the split. There are two cases based
* on the next byte:
*
* A) The next byte is LF
* The split needs to end after the current record is returned. The
* consumer of the next split will discard the first record, which
* is degenerate since LF is itself a delimiter, and start consuming
* records after that byte. If the current split tries to read
* another record then the record will be duplicated between splits.
*
* B) The next byte is not LF
* The current record will be returned but the stream will report
* the split has ended due to the peek into the next block. If the
* next record is not read then it will be lost, as the consumer of
* the next split will discard it before processing subsequent
* records. Therefore the next record beyond the reported split end
* must be consumed by this split to avoid data loss.
*
* 3) Last block of split ends at the beginning of a delimiter
* This is equivalent to case 1, as the reader will consume bytes into
* the next block and trigger the end of the split. No further records
* should be read as the consumer of the next split will discard the
* (degenerate) record at the beginning of its split.
*
* 4) Last block of split ends at the end of a delimiter
* Nothing special needs to be done here. The reader will not start
* examining the bytes into the next block until the next record is read,
* so the stream will not report the end of the split just yet. Once the
* next record is read then the next block will be accessed and the
* stream will indicate the end of the split. The consumer of the next
* split will correctly discard the first record of its split, and no
* data is lost or duplicated.
*
* If the default delimiter is used and the block ends at a CR then this
* is treated as case 2 since the reader does not yet know without
* looking at subsequent bytes whether the delimiter has ended.
*
* NOTE: It is assumed that compressed input streams *never* return bytes from
* multiple compressed blocks from a single read. Failure to do so will
* violate the buffering performed by this class, as it will access
* bytes into the next block after the split before returning all of the
* records from the previous block.
*/
@InterfaceAudience.Private
@InterfaceStability.Unstable
public class CompressedSplitLineReader extends SplitLineReader {
SplitCompressionInputStream scin;
private boolean usingCRLF;
private boolean needAdditionalRecord = false;
private boolean finished = false;
public CompressedSplitLineReader(SplitCompressionInputStream in,
Configuration conf,
byte[] recordDelimiterBytes)
throws IOException {
super(in, conf, recordDelimiterBytes);
scin = in;
usingCRLF = (recordDelimiterBytes == null);
}
@Override
protected int fillBuffer(InputStream in, byte[] buffer, boolean inDelimiter)
throws IOException {
int bytesRead = in.read(buffer);
// If the split ended in the middle of a record delimiter then we need
// to read one additional record, as the consumer of the next split will
// not recognize the partial delimiter as a record.
// However if using the default delimiter and the next character is a
// linefeed then next split will treat it as a delimiter all by itself
// and the additional record read should not be performed.
if (inDelimiter && bytesRead > 0) {
if (usingCRLF) {
needAdditionalRecord = (buffer[0] != '\n');
} else {
needAdditionalRecord = true;
}
}
return bytesRead;
}
@Override
public int readLine(Text str, int maxLineLength, int maxBytesToConsume)
throws IOException {
int bytesRead = 0;
if (!finished) {
// only allow at most one more record to be read after the stream
// reports the split ended
if (scin.getPos() > scin.getAdjustedEnd()) {
finished = true;
}
bytesRead = super.readLine(str, maxLineLength, maxBytesToConsume);
}
return bytesRead;
}
@Override
public boolean needAdditionalRecordAfterSplit() {
return !finished && needAdditionalRecord;
}
}

View File

@ -38,7 +38,6 @@ import org.apache.hadoop.io.compress.Decompressor;
import org.apache.hadoop.mapreduce.InputSplit; import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader; import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.util.LineReader;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
@ -55,7 +54,7 @@ public class LineRecordReader extends RecordReader<LongWritable, Text> {
private long start; private long start;
private long pos; private long pos;
private long end; private long end;
private LineReader in; private SplitLineReader in;
private FSDataInputStream fileIn; private FSDataInputStream fileIn;
private Seekable filePosition; private Seekable filePosition;
private int maxLineLength; private int maxLineLength;
@ -94,33 +93,19 @@ public class LineRecordReader extends RecordReader<LongWritable, Text> {
((SplittableCompressionCodec)codec).createInputStream( ((SplittableCompressionCodec)codec).createInputStream(
fileIn, decompressor, start, end, fileIn, decompressor, start, end,
SplittableCompressionCodec.READ_MODE.BYBLOCK); SplittableCompressionCodec.READ_MODE.BYBLOCK);
if (null == this.recordDelimiterBytes){ in = new CompressedSplitLineReader(cIn, job,
in = new LineReader(cIn, job); this.recordDelimiterBytes);
} else {
in = new LineReader(cIn, job, this.recordDelimiterBytes);
}
start = cIn.getAdjustedStart(); start = cIn.getAdjustedStart();
end = cIn.getAdjustedEnd(); end = cIn.getAdjustedEnd();
filePosition = cIn; filePosition = cIn;
} else { } else {
if (null == this.recordDelimiterBytes) { in = new SplitLineReader(codec.createInputStream(fileIn,
in = new LineReader(codec.createInputStream(fileIn, decompressor),
job);
} else {
in = new LineReader(codec.createInputStream(fileIn,
decompressor), job, this.recordDelimiterBytes); decompressor), job, this.recordDelimiterBytes);
}
filePosition = fileIn; filePosition = fileIn;
} }
} else { } else {
fileIn.seek(start); fileIn.seek(start);
if (null == this.recordDelimiterBytes){ in = new SplitLineReader(fileIn, job, this.recordDelimiterBytes);
in = new LineReader(fileIn, job);
} else {
in = new LineReader(fileIn, job, this.recordDelimiterBytes);
}
filePosition = fileIn; filePosition = fileIn;
} }
// If this is not the first split, we always throw away first record // If this is not the first split, we always throw away first record
@ -160,7 +145,7 @@ public class LineRecordReader extends RecordReader<LongWritable, Text> {
int newSize = 0; int newSize = 0;
// We always read one extra line, which lies outside the upper // We always read one extra line, which lies outside the upper
// split limit i.e. (end - 1) // split limit i.e. (end - 1)
while (getFilePosition() <= end) { while (getFilePosition() <= end || in.needAdditionalRecordAfterSplit()) {
newSize = in.readLine(value, maxLineLength, newSize = in.readLine(value, maxLineLength,
Math.max(maxBytesToConsume(pos), maxLineLength)); Math.max(maxBytesToConsume(pos), maxLineLength));
pos += newSize; pos += newSize;

View File

@ -0,0 +1,43 @@
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you 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 org.apache.hadoop.mapreduce.lib.input;
import java.io.IOException;
import java.io.InputStream;
import org.apache.hadoop.classification.InterfaceAudience;
import org.apache.hadoop.classification.InterfaceStability;
import org.apache.hadoop.conf.Configuration;
@InterfaceAudience.Private
@InterfaceStability.Unstable
public class SplitLineReader extends org.apache.hadoop.util.LineReader {
public SplitLineReader(InputStream in, byte[] recordDelimiterBytes) {
super(in, recordDelimiterBytes);
}
public SplitLineReader(InputStream in, Configuration conf,
byte[] recordDelimiterBytes) throws IOException {
super(in, conf, recordDelimiterBytes);
}
public boolean needAdditionalRecordAfterSplit() {
return false;
}
}

View File

@ -0,0 +1,100 @@
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you 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 org.apache.hadoop.mapred;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.junit.Test;
public class TestLineRecordReader {
private void testSplitRecords(String testFileName, long firstSplitLength)
throws IOException {
URL testFileUrl = getClass().getClassLoader().getResource(testFileName);
assertNotNull("Cannot find " + testFileName, testFileUrl);
File testFile = new File(testFileUrl.getFile());
long testFileSize = testFile.length();
Path testFilePath = new Path(testFile.getAbsolutePath());
Configuration conf = new Configuration();
conf.setInt(org.apache.hadoop.mapreduce.lib.input.
LineRecordReader.MAX_LINE_LENGTH, Integer.MAX_VALUE);
assertTrue("unexpected test data at " + testFile,
testFileSize > firstSplitLength);
// read the data without splitting to count the records
FileSplit split = new FileSplit(testFilePath, 0, testFileSize,
(String[])null);
LineRecordReader reader = new LineRecordReader(conf, split);
LongWritable key = new LongWritable();
Text value = new Text();
int numRecordsNoSplits = 0;
while (reader.next(key, value)) {
++numRecordsNoSplits;
}
reader.close();
// count the records in the first split
split = new FileSplit(testFilePath, 0, firstSplitLength, (String[])null);
reader = new LineRecordReader(conf, split);
int numRecordsFirstSplit = 0;
while (reader.next(key, value)) {
++numRecordsFirstSplit;
}
reader.close();
// count the records in the second split
split = new FileSplit(testFilePath, firstSplitLength,
testFileSize - firstSplitLength, (String[])null);
reader = new LineRecordReader(conf, split);
int numRecordsRemainingSplits = 0;
while (reader.next(key, value)) {
++numRecordsRemainingSplits;
}
reader.close();
assertEquals("Unexpected number of records in bzip2 compressed split",
numRecordsNoSplits, numRecordsFirstSplit + numRecordsRemainingSplits);
}
@Test
public void testBzip2SplitEndsAtCR() throws IOException {
// the test data contains a carriage-return at the end of the first
// split which ends at compressed offset 136498 and the next
// character is not a linefeed
testSplitRecords("blockEndingInCR.txt.bz2", 136498);
}
@Test
public void testBzip2SplitEndsAtCRThenLF() throws IOException {
// the test data contains a carriage-return at the end of the first
// split which ends at compressed offset 136498 and the next
// character is a linefeed
testSplitRecords("blockEndingInCRThenLF.txt.bz2", 136498);
}
}

View File

@ -0,0 +1,104 @@
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you 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 org.apache.hadoop.mapreduce.lib.input;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.TaskAttemptID;
import org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl;
import org.junit.Test;
public class TestLineRecordReader {
private void testSplitRecords(String testFileName, long firstSplitLength)
throws IOException {
URL testFileUrl = getClass().getClassLoader().getResource(testFileName);
assertNotNull("Cannot find " + testFileName, testFileUrl);
File testFile = new File(testFileUrl.getFile());
long testFileSize = testFile.length();
Path testFilePath = new Path(testFile.getAbsolutePath());
Configuration conf = new Configuration();
conf.setInt(org.apache.hadoop.mapreduce.lib.input.
LineRecordReader.MAX_LINE_LENGTH, Integer.MAX_VALUE);
assertTrue("unexpected test data at " + testFile,
testFileSize > firstSplitLength);
TaskAttemptContext context = new TaskAttemptContextImpl(conf, new TaskAttemptID());
// read the data without splitting to count the records
FileSplit split = new FileSplit(testFilePath, 0, testFileSize,
(String[])null);
LineRecordReader reader = new LineRecordReader();
reader.initialize(split, context);
int numRecordsNoSplits = 0;
while (reader.nextKeyValue()) {
++numRecordsNoSplits;
}
reader.close();
// count the records in the first split
split = new FileSplit(testFilePath, 0, firstSplitLength, (String[])null);
reader = new LineRecordReader();
reader.initialize(split, context);
int numRecordsFirstSplit = 0;
while (reader.nextKeyValue()) {
++numRecordsFirstSplit;
}
reader.close();
// count the records in the second split
split = new FileSplit(testFilePath, firstSplitLength,
testFileSize - firstSplitLength, (String[])null);
reader = new LineRecordReader();
reader.initialize(split, context);
int numRecordsRemainingSplits = 0;
while (reader.nextKeyValue()) {
++numRecordsRemainingSplits;
}
reader.close();
assertEquals("Unexpected number of records in bzip2 compressed split",
numRecordsNoSplits, numRecordsFirstSplit + numRecordsRemainingSplits);
}
@Test
public void testBzip2SplitEndsAtCR() throws IOException {
// the test data contains a carriage-return at the end of the first
// split which ends at compressed offset 136498 and the next
// character is not a linefeed
testSplitRecords("blockEndingInCR.txt.bz2", 136498);
}
@Test
public void testBzip2SplitEndsAtCRThenLF() throws IOException {
// the test data contains a carriage-return at the end of the first
// split which ends at compressed offset 136498 and the next
// character is a linefeed
testSplitRecords("blockEndingInCRThenLF.txt.bz2", 136498);
}
}