Michael Kamprath created SPARK-34563:
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Summary: Checkpointing a union with another checkpoint fails
Key: SPARK-34563
URL: https://issues.apache.org/jira/browse/SPARK-34563
Project: Spark
Issue Type: Bug
Components: PySpark
Affects Versions: 3.0.2
Environment: I am running Spark 3.0.2 in stand alone cluster mode,
built for Hadoop 2.7, and Scala 2.12.12. I am using QFS 2.2.2 (Quantcast File
System) as the underlying DFS. The nodes run on Debian Stretch, and Java is
openjdk version "1.8.0_275".
Reporter: Michael Kamprath
I have some PySpark code that periodically checkpoints a data frame that I am
building in pieces by union-ing those pieces together as they are constructed.
(Py)Spark fails on the second checkpoint, which would be a union of a new piece
of the desired data frame with a previously checkpointed piece. Some simplified
PySpark code that will trigger this problem is:
{code:java}
RANGE_STEP = 10000
PARTITIONS = 5
COUNT_UNIONS = 20
df = spark.range(1, RANGE_STEP+1, numPartitions=PARTITIONS)
for i in range(1, COUNT_UNIONS+1):
print('Processing i = {0}'.format(i))
new_df = spark.range(RANGE_STEP*i + 1, RANGE_STEP*(i+1) + 1,
numPartitions=PARTITIONS)
df = df.union(new_df).checkpoint()
df.count()
{code}
When this code gets to the checkpoint on the second loop iteration (i=2) the
job fails with an error:
{code:java}
Py4JJavaError: An error occurred while calling o119.checkpoint.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 9 in
stage 10.0 failed 4 times, most recent failure: Lost task 9.3 in stage 10.0
(TID 264, 10.20.30.13, executor 0): com.esotericsoftware.kryo.KryoException:
Encountered unregistered class ID: 9062
at
com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:137)
at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:693)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:804)
at
org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:296)
at
org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:168)
at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anon$1.hasNext(WholeStageCodegenExec.scala:729)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)
at org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1804)
at org.apache.spark.rdd.RDD.$anonfun$count$1(RDD.scala:1227)
at org.apache.spark.rdd.RDD.$anonfun$count$1$adapted(RDD.scala:1227)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2154)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:462)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:465)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2008)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2007)
at
scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at
scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:973)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:973)
at scala.Option.foreach(Option.scala:407)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2135)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2154)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2179)
at org.apache.spark.rdd.RDD.count(RDD.scala:1227)
at org.apache.spark.sql.Dataset.$anonfun$checkpoint$1(Dataset.scala:696)
at
org.apache.spark.sql.Dataset.$anonfun$withAction$1(Dataset.scala:3618)
at
org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$5(SQLExecution.scala:100)
at
org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
at
org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:87)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
at
org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
at org.apache.spark.sql.Dataset.checkpoint(Dataset.scala:687)
at org.apache.spark.sql.Dataset.checkpoint(Dataset.scala:650)
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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Caused by: com.esotericsoftware.kryo.KryoException: Encountered unregistered
class ID: 9062
at
com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:137)
at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:693)
at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:804)
at
org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:296)
at
org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:168)
at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anon$1.hasNext(WholeStageCodegenExec.scala:729)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)
at org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1804)
at org.apache.spark.rdd.RDD.$anonfun$count$1(RDD.scala:1227)
at org.apache.spark.rdd.RDD.$anonfun$count$1$adapted(RDD.scala:1227)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2154)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:462)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:465)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
... 1 more
{code}
Note that the checkpoint directory is set, as the first checkpoint does
succeed.
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