Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[SPARK-23207][SQL] Shuffle+Repartition on a DataFrame could lead to incorrect answers #20393

Closed
wants to merge 2 commits into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
Expand Up @@ -32,6 +32,8 @@ public abstract class RecordComparator {
public abstract int compare(
Object leftBaseObject,
long leftBaseOffset,
int leftBaseLength,
Object rightBaseObject,
long rightBaseOffset);
long rightBaseOffset,
int rightBaseLength);
}
Expand Up @@ -62,12 +62,13 @@ public int compare(RecordPointerAndKeyPrefix r1, RecordPointerAndKeyPrefix r2) {
int uaoSize = UnsafeAlignedOffset.getUaoSize();
if (prefixComparisonResult == 0) {
final Object baseObject1 = memoryManager.getPage(r1.recordPointer);
// skip length
final long baseOffset1 = memoryManager.getOffsetInPage(r1.recordPointer) + uaoSize;
final int baseLength1 = UnsafeAlignedOffset.getSize(baseObject1, baseOffset1 - uaoSize);
final Object baseObject2 = memoryManager.getPage(r2.recordPointer);
// skip length
final long baseOffset2 = memoryManager.getOffsetInPage(r2.recordPointer) + uaoSize;
return recordComparator.compare(baseObject1, baseOffset1, baseObject2, baseOffset2);
final int baseLength2 = UnsafeAlignedOffset.getSize(baseObject2, baseOffset2 - uaoSize);
return recordComparator.compare(baseObject1, baseOffset1, baseLength1, baseObject2,
baseOffset2, baseLength2);
} else {
return prefixComparisonResult;
}
Expand Down
Expand Up @@ -35,8 +35,8 @@ final class UnsafeSorterSpillMerger {
prefixComparator.compare(left.getKeyPrefix(), right.getKeyPrefix());
if (prefixComparisonResult == 0) {
return recordComparator.compare(
left.getBaseObject(), left.getBaseOffset(),
right.getBaseObject(), right.getBaseOffset());
left.getBaseObject(), left.getBaseOffset(), left.getRecordLength(),
right.getBaseObject(), right.getBaseOffset(), right.getRecordLength());
} else {
return prefixComparisonResult;
}
Expand Down
2 changes: 2 additions & 0 deletions core/src/main/scala/org/apache/spark/rdd/RDD.scala
Expand Up @@ -414,6 +414,8 @@ abstract class RDD[T: ClassTag](
*
* If you are decreasing the number of partitions in this RDD, consider using `coalesce`,
* which can avoid performing a shuffle.
*
* TODO Fix the Shuffle+Repartition data loss issue described in SPARK-23207.
*/
def repartition(numPartitions: Int)(implicit ord: Ordering[T] = null): RDD[T] = withScope {
coalesce(numPartitions, shuffle = true)
Expand Down
Expand Up @@ -72,8 +72,10 @@ public class UnsafeExternalSorterSuite {
public int compare(
Object leftBaseObject,
long leftBaseOffset,
int leftBaseLength,
Object rightBaseObject,
long rightBaseOffset) {
long rightBaseOffset,
int rightBaseLength) {
return 0;
}
};
Expand Down
Expand Up @@ -98,8 +98,10 @@ public void testSortingOnlyByIntegerPrefix() throws Exception {
public int compare(
Object leftBaseObject,
long leftBaseOffset,
int leftBaseLength,
Object rightBaseObject,
long rightBaseOffset) {
long rightBaseOffset,
int rightBaseLength) {
return 0;
}
};
Expand Down Expand Up @@ -164,8 +166,10 @@ public void freeAfterOOM() {
public int compare(
Object leftBaseObject,
long leftBaseOffset,
int leftBaseLength,
Object rightBaseObject,
long rightBaseOffset) {
long rightBaseOffset,
int rightBaseLength) {
return 0;
}
};
Expand Down
Expand Up @@ -222,7 +222,8 @@ class Word2VecSuite extends SparkFunSuite with MLlibTestSparkContext with Defaul
val oldModel = new OldWord2VecModel(word2VecMap)
val instance = new Word2VecModel("myWord2VecModel", oldModel)
val newInstance = testDefaultReadWrite(instance)
assert(newInstance.getVectors.collect() === instance.getVectors.collect())
assert(newInstance.getVectors.collect().sortBy(_.getString(0)) ===
instance.getVectors.collect().sortBy(_.getString(0)))
}

test("Word2Vec works with input that is non-nullable (NGram)") {
Expand Down
@@ -0,0 +1,70 @@
/*
* 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.spark.sql.execution;

import org.apache.spark.unsafe.Platform;
import org.apache.spark.util.collection.unsafe.sort.RecordComparator;

public final class RecordBinaryComparator extends RecordComparator {

// TODO(jiangxb) Add test suite for this.
@Override
public int compare(
Object leftObj, long leftOff, int leftLen, Object rightObj, long rightOff, int rightLen) {
int i = 0;
int res = 0;

// If the arrays have different length, the longer one is larger.
if (leftLen != rightLen) {
return leftLen - rightLen;
}

// The following logic uses `leftLen` as the length for both `leftObj` and `rightObj`, since
// we have guaranteed `leftLen` == `rightLen`.

// check if stars align and we can get both offsets to be aligned
if ((leftOff % 8) == (rightOff % 8)) {
while ((leftOff + i) % 8 != 0 && i < leftLen) {
res = (Platform.getByte(leftObj, leftOff + i) & 0xff) -
(Platform.getByte(rightObj, rightOff + i) & 0xff);
if (res != 0) return res;
i += 1;
}
}
// for architectures that support unaligned accesses, chew it up 8 bytes at a time
if (Platform.unaligned() || (((leftOff + i) % 8 == 0) && ((rightOff + i) % 8 == 0))) {
while (i <= leftLen - 8) {
res = (int) ((Platform.getLong(leftObj, leftOff + i) -
Platform.getLong(rightObj, rightOff + i)) % Integer.MAX_VALUE);
if (res != 0) return res;
i += 8;
}
}
// this will finish off the unaligned comparisons, or do the entire aligned comparison
// whichever is needed.
while (i < leftLen) {
res = (Platform.getByte(leftObj, leftOff + i) & 0xff) -
(Platform.getByte(rightObj, rightOff + i) & 0xff);
if (res != 0) return res;
i += 1;
}

// The two arrays are equal.
return 0;
}
}
Expand Up @@ -18,7 +18,9 @@
package org.apache.spark.sql.execution;

import java.io.IOException;
import java.util.function.Supplier;

import org.apache.spark.sql.catalyst.util.TypeUtils;
import scala.collection.AbstractIterator;
import scala.collection.Iterator;
import scala.math.Ordering;
Expand Down Expand Up @@ -56,26 +58,50 @@ public abstract static class PrefixComputer {

public static class Prefix {
/** Key prefix value, or the null prefix value if isNull = true. **/
long value;
public long value;

/** Whether the key is null. */
boolean isNull;
public boolean isNull;
}

/**
* Computes prefix for the given row. For efficiency, the returned object may be reused in
* further calls to a given PrefixComputer.
*/
abstract Prefix computePrefix(InternalRow row);
public abstract Prefix computePrefix(InternalRow row);
}

public UnsafeExternalRowSorter(
public static UnsafeExternalRowSorter createWithRecordComparator(
StructType schema,
Supplier<RecordComparator> recordComparatorSupplier,
PrefixComparator prefixComparator,
PrefixComputer prefixComputer,
long pageSizeBytes,
boolean canUseRadixSort) throws IOException {
return new UnsafeExternalRowSorter(schema, recordComparatorSupplier, prefixComparator,
prefixComputer, pageSizeBytes, canUseRadixSort);
}

public static UnsafeExternalRowSorter create(
StructType schema,
Ordering<InternalRow> ordering,
PrefixComparator prefixComparator,
PrefixComputer prefixComputer,
long pageSizeBytes,
boolean canUseRadixSort) throws IOException {
Supplier<RecordComparator> recordComparatorSupplier =
() -> new RowComparator(ordering, schema.length());
return new UnsafeExternalRowSorter(schema, recordComparatorSupplier, prefixComparator,
prefixComputer, pageSizeBytes, canUseRadixSort);
}

private UnsafeExternalRowSorter(
StructType schema,
Supplier<RecordComparator> recordComparatorSupplier,
PrefixComparator prefixComparator,
PrefixComputer prefixComputer,
long pageSizeBytes,
boolean canUseRadixSort) throws IOException {
this.schema = schema;
this.prefixComputer = prefixComputer;
final SparkEnv sparkEnv = SparkEnv.get();
Expand All @@ -85,7 +111,7 @@ public UnsafeExternalRowSorter(
sparkEnv.blockManager(),
sparkEnv.serializerManager(),
taskContext,
() -> new RowComparator(ordering, schema.length()),
recordComparatorSupplier,
prefixComparator,
sparkEnv.conf().getInt("spark.shuffle.sort.initialBufferSize",
DEFAULT_INITIAL_SORT_BUFFER_SIZE),
Expand Down Expand Up @@ -206,7 +232,13 @@ private static final class RowComparator extends RecordComparator {
}

@Override
public int compare(Object baseObj1, long baseOff1, Object baseObj2, long baseOff2) {
public int compare(
Object baseObj1,
long baseOff1,
int baseLen1,
Object baseObj2,
long baseOff2,
int baseLen2) {
// Note that since ordering doesn't need the total length of the record, we just pass 0
// into the row.
row1.pointTo(baseObj1, baseOff1, 0);
Expand Down
Expand Up @@ -1128,6 +1128,18 @@ object SQLConf {
.checkValues(PartitionOverwriteMode.values.map(_.toString))
.createWithDefault(PartitionOverwriteMode.STATIC.toString)

val SORT_BEFORE_REPARTITION =
buildConf("spark.sql.execution.sortBeforeRepartition")
.internal()
.doc("When perform a repartition following a shuffle, the output row ordering would be " +
"nondeterministic. If some downstream stages fail and some tasks of the repartition " +
"stage retry, these tasks may generate different data, and that can lead to correctness " +
"issues. Turn on this config to insert a local sort before actually doing repartition " +
"to generate consistent repartition results. The performance of repartition() may go " +
"down since we insert extra local sort before it.")
.booleanConf
.createWithDefault(true)

object Deprecated {
val MAPRED_REDUCE_TASKS = "mapred.reduce.tasks"
}
Expand Down Expand Up @@ -1278,6 +1290,8 @@ class SQLConf extends Serializable with Logging {

def stringRedationPattern: Option[Regex] = SQL_STRING_REDACTION_PATTERN.readFrom(reader)

def sortBeforeRepartition: Boolean = getConf(SORT_BEFORE_REPARTITION)

/**
* Returns the [[Resolver]] for the current configuration, which can be used to determine if two
* identifiers are equal.
Expand Down
Expand Up @@ -241,7 +241,13 @@ private static final class KVComparator extends RecordComparator {
}

@Override
public int compare(Object baseObj1, long baseOff1, Object baseObj2, long baseOff2) {
public int compare(
Object baseObj1,
long baseOff1,
int baseLen1,
Object baseObj2,
long baseOff2,
int baseLen2) {
// Note that since ordering doesn't need the total length of the record, we just pass 0
// into the row.
row1.pointTo(baseObj1, baseOff1 + 4, 0);
Expand Down
Expand Up @@ -84,7 +84,7 @@ case class SortExec(
}

val pageSize = SparkEnv.get.memoryManager.pageSizeBytes
val sorter = new UnsafeExternalRowSorter(
val sorter = UnsafeExternalRowSorter.create(
schema, ordering, prefixComparator, prefixComputer, pageSize, canUseRadixSort)

if (testSpillFrequency > 0) {
Expand Down
Expand Up @@ -18,20 +18,23 @@
package org.apache.spark.sql.execution.exchange

import java.util.Random
import java.util.function.Supplier

import org.apache.spark._
import org.apache.spark.rdd.RDD
import org.apache.spark.serializer.Serializer
import org.apache.spark.shuffle.sort.SortShuffleManager
import org.apache.spark.sql.catalyst.InternalRow
import org.apache.spark.sql.catalyst.errors._
import org.apache.spark.sql.catalyst.expressions.{Attribute, UnsafeProjection}
import org.apache.spark.sql.catalyst.expressions.{Attribute, UnsafeProjection, UnsafeRow}
import org.apache.spark.sql.catalyst.expressions.codegen.LazilyGeneratedOrdering
import org.apache.spark.sql.catalyst.plans.physical._
import org.apache.spark.sql.execution._
import org.apache.spark.sql.execution.metric.SQLMetrics
import org.apache.spark.sql.internal.SQLConf
import org.apache.spark.sql.types.StructType
import org.apache.spark.util.MutablePair
import org.apache.spark.util.collection.unsafe.sort.{PrefixComparators, RecordComparator}

/**
* Performs a shuffle that will result in the desired `newPartitioning`.
Expand Down Expand Up @@ -247,14 +250,57 @@ object ShuffleExchangeExec {
case RangePartitioning(_, _) | SinglePartition => identity
case _ => sys.error(s"Exchange not implemented for $newPartitioning")
}

val rddWithPartitionIds: RDD[Product2[Int, InternalRow]] = {
if (needToCopyObjectsBeforeShuffle(part, serializer)) {
// [SPARK-23207] Have to make sure the generated RoundRobinPartitioning is deterministic,
// otherwise a retry task may output different rows and thus lead to data loss.
//
// Currently we following the most straight-forward way that perform a local sort before
// partitioning.
val newRdd = if (SQLConf.get.sortBeforeRepartition &&
newPartitioning.isInstanceOf[RoundRobinPartitioning]) {
rdd.mapPartitionsInternal { iter =>
val recordComparatorSupplier = new Supplier[RecordComparator] {
override def get: RecordComparator = new RecordBinaryComparator()
}
// The comparator for comparing row hashcode, which should always be Integer.
val prefixComparator = PrefixComparators.LONG
val canUseRadixSort = SparkEnv.get.conf.get(SQLConf.RADIX_SORT_ENABLED)
// The prefix computer generates row hashcode as the prefix, so we may decrease the
// probability that the prefixes are equal when input rows choose column values from a
// limited range.
val prefixComputer = new UnsafeExternalRowSorter.PrefixComputer {
private val result = new UnsafeExternalRowSorter.PrefixComputer.Prefix
override def computePrefix(row: InternalRow):
UnsafeExternalRowSorter.PrefixComputer.Prefix = {
// The hashcode generated from the binary form of a [[UnsafeRow]] should not be null.
result.isNull = false
result.value = row.hashCode()
result
}
}
val pageSize = SparkEnv.get.memoryManager.pageSizeBytes

val sorter = UnsafeExternalRowSorter.createWithRecordComparator(
StructType.fromAttributes(outputAttributes),
recordComparatorSupplier,
prefixComparator,
prefixComputer,
pageSize,
canUseRadixSort)
sorter.sort(iter.asInstanceOf[Iterator[UnsafeRow]])
}
} else {
rdd
}

if (needToCopyObjectsBeforeShuffle(part, serializer)) {
newRdd.mapPartitionsInternal { iter =>
val getPartitionKey = getPartitionKeyExtractor()
iter.map { row => (part.getPartition(getPartitionKey(row)), row.copy()) }
}
} else {
rdd.mapPartitionsInternal { iter =>
newRdd.mapPartitionsInternal { iter =>
val getPartitionKey = getPartitionKeyExtractor()
val mutablePair = new MutablePair[Int, InternalRow]()
iter.map { row => mutablePair.update(part.getPartition(getPartitionKey(row)), row) }
Expand Down