Kaushal Prajapati created SPARK-22458:
-----------------------------------------
Summary: OutOfDirectMemoryError with Spark 2.2
Key: SPARK-22458
URL: https://issues.apache.org/jira/browse/SPARK-22458
Project: Spark
Issue Type: Bug
Components: Shuffle, SQL, YARN
Affects Versions: 2.2.0
Reporter: Kaushal Prajapati
Priority: Blocker
We were using Spark 2.1 from last 6 months to execute multiple spark jobs that
is running 15 hour long for 50+ TB of source data with below configurations
successfully.
spark.master yarn
spark.driver.cores 10
spark.driver.maxResultSize 5g
spark.driver.memory 20g
spark.executor.cores 5
spark.executor.extraJavaOptions -XX:+UseG1GC
*-Dio.netty.maxDirectMemory=1024* -XX:MaxGCPauseMillis=60000
*-XX:MaxDirectMemorySize=2048m*
-Dlog4j.configuration=file:///conf/log4j.properties -Dhdp.version=2.5.3.0-37
spark.driver.extraJavaOptions *
-Dio.netty.maxDirectMemory=2048 -XX:MaxDirectMemorySize=2048m*
-Dlog4j.configuration=file:///conf/log4j.properties -Dhdp.version=2.5.3.0-37
spark.executor.instances 30
spark.executor.memory 30g
*spark.kryoserializer.buffer.max 512m*
spark.network.timeout 12000s
spark.serializer
org.apache.spark.serializer.KryoSerializer
spark.shuffle.io.preferDirectBufs false
spark.sql.catalogImplementation hive
spark.sql.shuffle.partitions 5000
spark.yarn.driver.memoryOverhead 1536
spark.yarn.executor.memoryOverhead 4096
spark.core.connection.ack.wait.timeout 600s
spark.scheduler.maxRegisteredResourcesWaitingTime 15s
spark.sql.hive.filesourcePartitionFileCacheSize 524288000
spark.dynamicAllocation.executorIdleTimeout 30000s
spark.dynamicAllocation.enabled true
spark.hadoop.yarn.timeline-service.enabled false
spark.shuffle.service.enabled true
spark.yarn.am.extraJavaOptions -Dhdp.version=2.5.3.0-37 *
-Dio.netty.maxDirectMemory=1024 -XX:MaxDirectMemorySize=1024m*
Recently we tried to upgrade from Spark 2.1 to Spark 2.2 to get some fixes
using latest version. But we started facing DirectBuffer outOfMemory error and
exceeding memory limits for executor memoryOverhead issue. To fix that we
started tweaking multiple properties but still issue persists. Relevant
information is shared below
Please let me any other details is requried,
Snapshot for DirectMemory Error Stacktrace :-
10:48:26.417 WARN org.apache.spark.scheduler.TaskSetManager: Lost task 5.0 in
stage 5.3 (TID 25022, dedwdprshc070.de.xxxxxxx.com, executor 615):
FetchFailed(BlockManagerId(465, dedwdprshc061.de.xxxxxxx.com, 7337, None),
shuffleId=7, mapId=141, reduceId=3372, message=
org.apache.spark.shuffle.FetchFailedException: failed to allocate 65536 byte(s)
of direct memory (used: 1073699840, max: 1073741824)
at
org.apache.spark.storage.ShuffleBlockFetcherIterator.throwFetchFailedException(ShuffleBlockFetcherIterator.scala:442)
at
org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:418)
at
org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:59)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at
org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
at
org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:37)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.sort_addToSorter$(Unknown
Source)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.findNextInnerJoinRows$(Unknown
Source)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$2.hasNext(WholeStageCodegenExec.scala:414)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at
org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:166)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
Caused by: io.netty.util.internal.OutOfDirectMemoryError: failed to allocate
65536 byte(s) of direct memory (used: 1073699840, max: 1073741824)
at
io.netty.util.internal.PlatformDependent.incrementMemoryCounter(PlatformDependent.java:530)
at
io.netty.util.internal.PlatformDependent.allocateDirectNoCleaner(PlatformDependent.java:484)
at
io.netty.buffer.UnpooledUnsafeNoCleanerDirectByteBuf.allocateDirect(UnpooledUnsafeNoCleanerDirectByteBuf.java:30)
at
io.netty.buffer.UnpooledUnsafeDirectByteBuf.<init>(UnpooledUnsafeDirectByteBuf.java:67)
at
io.netty.buffer.UnpooledUnsafeNoCleanerDirectByteBuf.<init>(UnpooledUnsafeNoCleanerDirectByteBuf.java:25)
at
io.netty.buffer.UnsafeByteBufUtil.newUnsafeDirectByteBuf(UnsafeByteBufUtil.java:425)
at
io.netty.buffer.PooledByteBufAllocator.newDirectBuffer(PooledByteBufAllocator.java:299)
at
io.netty.buffer.AbstractByteBufAllocator.directBuffer(AbstractByteBufAllocator.java:177)
at
io.netty.buffer.AbstractByteBufAllocator.directBuffer(AbstractByteBufAllocator.java:168)
at
io.netty.buffer.AbstractByteBufAllocator.ioBuffer(AbstractByteBufAllocator.java:129)
at
io.netty.channel.AdaptiveRecvByteBufAllocator$HandleImpl.allocate(AdaptiveRecvByteBufAllocator.java:104)
at
io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:117)
at
io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at
io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at
io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
... 1 more
if i removed above netty configuration, getting below error
Snapshot for Excedding memory overhead Stacktrace :-
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure:
Task 3372 in stage 5.0 failed 4 times, most recent failure: Lost task 3372.3 in
stage 5.0 (TID 19534, dedwfprshd006.de.xxxxxxx.com, executor 125):
ExecutorLostFailure (executor 125 exited caused by one of the running tasks)
Reason: Container killed by YARN for exceeding memory limits. 37.1 GB of 34 GB
physical memory used. Consider boosting spark.yarn.executor.memoryOverhead.
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
at
scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at scala.Option.foreach(Option.scala:257)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
at
org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:188)
... 49 more
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