[SPARK-24002] [SQL] Task not serializable caused by org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytes #21086
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LGTM |
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Test build #89464 has finished for PR 21086 at commit
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Thanks! Merged to master |
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If the community hit this issue, we can then backport it to Spark 2.3. |
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I'm hitting this issue after upgrading from 2.0.2 to 2.3.0. Please backport this PR to Spark 2.3.0 |
ghoto
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May 16, 2018
| (file: PartitionedFile) => { | ||
| assert(file.partitionValues.numFields == partitionSchema.size) | ||
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| // Try to push down filters when filter push-down is enabled. |
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So this code is the same as before. How can this solve the bug described in the head of the Conversation?
@gatorsmile
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Now the code is inside the read function, which will be executed at executor side. Thus we don't need to serialize ParquetFilters.
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since people hit this issue, let's backport. cc @gatorsmile |
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@ghoto Sure. Will backport it tonight. |
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….io.api.Binary$ByteBufferBackedBinary.getBytes ``` Py4JJavaError: An error occurred while calling o153.sql. : org.apache.spark.SparkException: Job aborted. at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:223) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:189) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:70) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:68) at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:79) at org.apache.spark.sql.Dataset$$anonfun$6.apply(Dataset.scala:190) at org.apache.spark.sql.Dataset$$anonfun$6.apply(Dataset.scala:190) at org.apache.spark.sql.Dataset$$anonfun$59.apply(Dataset.scala:3021) at org.apache.spark.sql.execution.SQLExecution$.withCustomExecutionEnv(SQLExecution.scala:89) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:127) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3020) at org.apache.spark.sql.Dataset.<init>(Dataset.scala:190) at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:74) at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:646) at sun.reflect.GeneratedMethodAccessor153.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:380) at py4j.Gateway.invoke(Gateway.java:293) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:226) at java.lang.Thread.run(Thread.java:748) Caused by: org.apache.spark.SparkException: Exception thrown in Future.get: at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec.doExecuteBroadcast(BroadcastExchangeExec.scala:190) at org.apache.spark.sql.execution.InputAdapter.doExecuteBroadcast(WholeStageCodegenExec.scala:267) at org.apache.spark.sql.execution.joins.BroadcastNestedLoopJoinExec.doConsume(BroadcastNestedLoopJoinExec.scala:530) at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:155) at org.apache.spark.sql.execution.ProjectExec.consume(basicPhysicalOperators.scala:37) at org.apache.spark.sql.execution.ProjectExec.doConsume(basicPhysicalOperators.scala:69) at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:155) at org.apache.spark.sql.execution.FilterExec.consume(basicPhysicalOperators.scala:144) ... at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:190) ... 23 more Caused by: java.util.concurrent.ExecutionException: org.apache.spark.SparkException: Task not serializable at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:206) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec.doExecuteBroadcast(BroadcastExchangeExec.scala:179) ... 276 more Caused by: org.apache.spark.SparkException: Task not serializable at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:340) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:330) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2380) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1.apply(RDD.scala:850) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1.apply(RDD.scala:849) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:371) at org.apache.spark.rdd.RDD.mapPartitionsWithIndex(RDD.scala:849) at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:417) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.prepareShuffleDependency(ShuffleExchangeExec.scala:89) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:125) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:116) at org.apache.spark.sql.catalyst.errors.package$.attachTree(package.scala:52) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.doExecute(ShuffleExchangeExec.scala:116) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:271) at org.apache.spark.sql.execution.aggregate.HashAggregateExec.inputRDDs(HashAggregateExec.scala:181) at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:414) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:61) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:70) at org.apache.spark.sql.execution.SparkPlan.executeCollectResult(SparkPlan.scala:264) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1$$anonfun$call$1.apply(BroadcastExchangeExec.scala:93) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1$$anonfun$call$1.apply(BroadcastExchangeExec.scala:81) at org.apache.spark.sql.execution.SQLExecution$.withExecutionId(SQLExecution.scala:150) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1.call(BroadcastExchangeExec.scala:80) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1.call(BroadcastExchangeExec.scala:76) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.nio.BufferUnderflowException at java.nio.HeapByteBuffer.get(HeapByteBuffer.java:151) at java.nio.ByteBuffer.get(ByteBuffer.java:715) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytes(Binary.java:405) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytesUnsafe(Binary.java:414) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.writeObject(Binary.java:484) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1128) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496) ``` The Parquet filters are serializable but not thread safe. SparkPlan.prepare() could be called in different threads (BroadcastExchange will call it in a thread pool). Thus, we could serialize the same Parquet filter at the same time. This is not easily reproduced. The fix is to avoid serializing these Parquet filters in the driver. This PR is to avoid serializing these Parquet filters by moving the parquet filter generation from the driver to executors. Having two queries one is a 1000-line SQL query and a 3000-line SQL query. Need to run at least one hour with a heavy write workload to reproduce once. Author: gatorsmile <[email protected]> Closes apache#21086 from gatorsmile/taskNotSerializable.
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May 17, 2018
…apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytes This PR is to backport #21086 to Apache Spark 2.3 ---- ``` Py4JJavaError: An error occurred while calling o153.sql. : org.apache.spark.SparkException: Job aborted. at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:223) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:189) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:70) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:68) at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:79) at org.apache.spark.sql.Dataset$$anonfun$6.apply(Dataset.scala:190) at org.apache.spark.sql.Dataset$$anonfun$6.apply(Dataset.scala:190) at org.apache.spark.sql.Dataset$$anonfun$59.apply(Dataset.scala:3021) at org.apache.spark.sql.execution.SQLExecution$.withCustomExecutionEnv(SQLExecution.scala:89) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:127) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3020) at org.apache.spark.sql.Dataset.<init>(Dataset.scala:190) at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:74) at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:646) at sun.reflect.GeneratedMethodAccessor153.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:380) at py4j.Gateway.invoke(Gateway.java:293) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:226) at java.lang.Thread.run(Thread.java:748) Caused by: org.apache.spark.SparkException: Exception thrown in Future.get: at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec.doExecuteBroadcast(BroadcastExchangeExec.scala:190) at org.apache.spark.sql.execution.InputAdapter.doExecuteBroadcast(WholeStageCodegenExec.scala:267) at org.apache.spark.sql.execution.joins.BroadcastNestedLoopJoinExec.doConsume(BroadcastNestedLoopJoinExec.scala:530) at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:155) at org.apache.spark.sql.execution.ProjectExec.consume(basicPhysicalOperators.scala:37) at org.apache.spark.sql.execution.ProjectExec.doConsume(basicPhysicalOperators.scala:69) at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:155) at org.apache.spark.sql.execution.FilterExec.consume(basicPhysicalOperators.scala:144) ... at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:190) ... 23 more Caused by: java.util.concurrent.ExecutionException: org.apache.spark.SparkException: Task not serializable at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:206) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec.doExecuteBroadcast(BroadcastExchangeExec.scala:179) ... 276 more Caused by: org.apache.spark.SparkException: Task not serializable at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:340) at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:330) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:156) at org.apache.spark.SparkContext.clean(SparkContext.scala:2380) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1.apply(RDD.scala:850) at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1.apply(RDD.scala:849) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:371) at org.apache.spark.rdd.RDD.mapPartitionsWithIndex(RDD.scala:849) at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:417) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.prepareShuffleDependency(ShuffleExchangeExec.scala:89) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:125) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$$anonfun$doExecute$1.apply(ShuffleExchangeExec.scala:116) at org.apache.spark.sql.catalyst.errors.package$.attachTree(package.scala:52) at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec.doExecute(ShuffleExchangeExec.scala:116) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:271) at org.apache.spark.sql.execution.aggregate.HashAggregateExec.inputRDDs(HashAggregateExec.scala:181) at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:414) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:123) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:118) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$3.apply(SparkPlan.scala:152) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:149) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:118) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:61) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:70) at org.apache.spark.sql.execution.SparkPlan.executeCollectResult(SparkPlan.scala:264) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1$$anonfun$call$1.apply(BroadcastExchangeExec.scala:93) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1$$anonfun$call$1.apply(BroadcastExchangeExec.scala:81) at org.apache.spark.sql.execution.SQLExecution$.withExecutionId(SQLExecution.scala:150) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1.call(BroadcastExchangeExec.scala:80) at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec$$anon$1.call(BroadcastExchangeExec.scala:76) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.nio.BufferUnderflowException at java.nio.HeapByteBuffer.get(HeapByteBuffer.java:151) at java.nio.ByteBuffer.get(ByteBuffer.java:715) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytes(Binary.java:405) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.getBytesUnsafe(Binary.java:414) at org.apache.parquet.io.api.Binary$ByteBufferBackedBinary.writeObject(Binary.java:484) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:1128) at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1496) ``` The Parquet filters are serializable but not thread safe. SparkPlan.prepare() could be called in different threads (BroadcastExchange will call it in a thread pool). Thus, we could serialize the same Parquet filter at the same time. This is not easily reproduced. The fix is to avoid serializing these Parquet filters in the driver. This PR is to avoid serializing these Parquet filters by moving the parquet filter generation from the driver to executors. ## How was this patch tested? Having two queries one is a 1000-line SQL query and a 3000-line SQL query. Need to run at least one hour with a heavy write workload to reproduce once. Author: gatorsmile <[email protected]> Closes #21351 from gatorsmile/backportSPARK-24002.
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What changes were proposed in this pull request?
The Parquet filters are serializable but not thread safe. SparkPlan.prepare() could be called in different threads (BroadcastExchange will call it in a thread pool). Thus, we could serialize the same Parquet filter at the same time. This is not easily reproduced. The fix is to avoid serializing these Parquet filters in the driver. This PR is to avoid serializing these Parquet filters by moving the parquet filter generation from the driver to executors.
How was this patch tested?
Having two queries one is a 1000-line SQL query and a 3000-line SQL query. Need to run at least one hour with a heavy write workload to reproduce once.