[
https://issues.apache.org/jira/browse/SPARK-19809?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16734510#comment-16734510
]
Prashanth Sandela commented on SPARK-19809:
-------------------------------------------
[~dongjoon] I'm encountering same similar issue with spark version 2.3.1
I'm trying to read from a table which was ingested by sqoop. There are few 0
byte files for this table. The file sizes looks like below:
{noformat}
-rw-rw-r-- 3 cloud-user root 17.3 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00000
-rw-rw-r-- 3 cloud-user root 10.3 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00001
-rw-rw-r-- 3 cloud-user root 19.9 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00002
-rw-rw-r-- 3 cloud-user root 13.0 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00003
-rw-rw-r-- 3 cloud-user root 0 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00004
-rw-rw-r-- 3 cloud-user root 3.4 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00005
-rw-rw-r-- 3 cloud-user root 13.8 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00006
-rw-rw-r-- 3 cloud-user root 0 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00007
-rw-rw-r-- 3 cloud-user root 0 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00008
-rw-rw-r-- 3 cloud-user root 6.9 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00009
-rw-rw-r-- 3 cloud-user root 9.0 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00010
-rw-rw-r-- 3 cloud-user root 11.4 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00011
-rw-rw-r-- 3 cloud-user root 14.7 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00012
-rw-rw-r-- 3 cloud-user root 17.4 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00013
-rw-rw-r-- 3 cloud-user root 17.1 M 2019-01-03 22:20
/apps/hive/warehouse/default.db/table_with_few_zero_byte_files/part-m-00014{noformat}
Spark throws exception while doing count
{noformat}
scala> spark.read.table("table_with_few_zero_byte_files").show()
java.lang.RuntimeException: serious problem at
org.apache.hadoop.hive.ql.io.orc.OrcInputFormat.generateSplitsInfo(OrcInputFormat.java:1021)
at
org.apache.hadoop.hive.ql.io.orc.OrcInputFormat.getSplits(OrcInputFormat.java:1048)
at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:200) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:253) at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:251) at
scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.rdd.RDD.partitions(RDD.scala:251) at
org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:340) at
org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
at
org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3273)
at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484) at
org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484) at
org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3254) at
org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3253) at
org.apache.spark.sql.Dataset.head(Dataset.scala:2484) at
org.apache.spark.sql.Dataset.take(Dataset.scala:2698) at
org.apache.spark.sql.Dataset.showString(Dataset.scala:254) at
org.apache.spark.sql.Dataset.show(Dataset.scala:723) at
org.apache.spark.sql.Dataset.show(Dataset.scala:682) at
org.apache.spark.sql.Dataset.show(Dataset.scala:691) ... 49 elided Caused by:
java.lang.NullPointerException at
org.apache.hadoop.hive.ql.io.orc.OrcInputFormat$BISplitStrategy.getSplits(OrcInputFormat.java:560)
at
org.apache.hadoop.hive.ql.io.orc.OrcInputFormat.generateSplitsInfo(OrcInputFormat.java:1010)
... 99 more
scala> sql("set spark.sql.hive.convertMetastoreOrc=true")
res22: org.apache.spark.sql.DataFrame = [key: string, value: string]
scala> spark.read.table("table_with_few_zero_byte_files").show()
java.lang.IndexOutOfBoundsException at
java.nio.Buffer.checkIndex(Buffer.java:540) at
java.nio.HeapByteBuffer.get(HeapByteBuffer.java:139) at
org.apache.hadoop.hive.ql.io.orc.ReaderImpl.extractMetaInfoFromFooter(ReaderImpl.java:377)
at org.apache.hadoop.hive.ql.io.orc.ReaderImpl.<init>(ReaderImpl.java:319) at
org.apache.hadoop.hive.ql.io.orc.OrcFile.createReader(OrcFile.java:187) at
org.apache.spark.sql.hive.orc.OrcFileOperator$$anonfun$getFileReader$2.apply(OrcFileOperator.scala:75)
at
org.apache.spark.sql.hive.orc.OrcFileOperator$$anonfun$getFileReader$2.apply(OrcFileOperator.scala:73)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409) at
scala.collection.TraversableOnce$class.collectFirst(TraversableOnce.scala:145)
at scala.collection.AbstractIterator.collectFirst(Iterator.scala:1336) at
org.apache.spark.sql.hive.orc.OrcFileOperator$.getFileReader(OrcFileOperator.scala:86)
at
org.apache.spark.sql.hive.orc.OrcFileOperator$$anonfun$readSchema$1.apply(OrcFileOperator.scala:95)
at
org.apache.spark.sql.hive.orc.OrcFileOperator$$anonfun$readSchema$1.apply(OrcFileOperator.scala:95)
at
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241)
at
scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241)
at scala.collection.immutable.List.foreach(List.scala:381) at
scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:241) at
scala.collection.immutable.List.flatMap(List.scala:344) at
org.apache.spark.sql.hive.orc.OrcFileOperator$.readSchema(OrcFileOperator.scala:95)
at
org.apache.spark.sql.hive.orc.OrcFileFormat.inferSchema(OrcFileFormat.scala:63)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog.org$apache$spark$sql$hive$HiveMetastoreCatalog$$inferIfNeeded(HiveMetastoreCatalog.scala:239)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog$$anonfun$6$$anonfun$7.apply(HiveMetastoreCatalog.scala:193)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog$$anonfun$6$$anonfun$7.apply(HiveMetastoreCatalog.scala:192)
at scala.Option.getOrElse(Option.scala:121) at
org.apache.spark.sql.hive.HiveMetastoreCatalog$$anonfun$6.apply(HiveMetastoreCatalog.scala:192)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog$$anonfun$6.apply(HiveMetastoreCatalog.scala:185)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog.withTableCreationLock(HiveMetastoreCatalog.scala:54)
at
org.apache.spark.sql.hive.HiveMetastoreCatalog.convertToLogicalRelation(HiveMetastoreCatalog.scala:185)
at
org.apache.spark.sql.hive.RelationConversions.org$apache$spark$sql$hive$RelationConversions$$convert(HiveStrategies.scala:205)
at
org.apache.spark.sql.hive.RelationConversions$$anonfun$apply$4.applyOrElse(HiveStrategies.scala:226)
at
org.apache.spark.sql.hive.RelationConversions$$anonfun$apply$4.applyOrElse(HiveStrategies.scala:215)
at
org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$1.apply(TreeNode.scala:289)
at
org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$1.apply(TreeNode.scala:289)
at
org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:70)
at
org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:288) at
org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$3.apply(TreeNode.scala:286)
at
org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$3.apply(TreeNode.scala:286)
at
org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:306)
at
org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:187)
at
org.apache.spark.sql.catalyst.trees.TreeNode.mapChildren(TreeNode.scala:304) at
org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:286) at
org.apache.spark.sql.hive.RelationConversions.apply(HiveStrategies.scala:215)
at
org.apache.spark.sql.hive.RelationConversions.apply(HiveStrategies.scala:180)
at
org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1$$anonfun$apply$1.apply(RuleExecutor.scala:87)
at
org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1$$anonfun$apply$1.apply(RuleExecutor.scala:84)
at
scala.collection.IndexedSeqOptimized$class.foldl(IndexedSeqOptimized.scala:57)
at
scala.collection.IndexedSeqOptimized$class.foldLeft(IndexedSeqOptimized.scala:66)
at scala.collection.mutable.ArrayBuffer.foldLeft(ArrayBuffer.scala:48) at
org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1.apply(RuleExecutor.scala:84)
at
org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1.apply(RuleExecutor.scala:76)
at scala.collection.immutable.List.foreach(List.scala:381) at
org.apache.spark.sql.catalyst.rules.RuleExecutor.execute(RuleExecutor.scala:76)
at
org.apache.spark.sql.catalyst.analysis.Analyzer.org$apache$spark$sql$catalyst$analysis$Analyzer$$executeSameContext(Analyzer.scala:124)
at org.apache.spark.sql.catalyst.analysis.Analyzer.execute(Analyzer.scala:118)
at
org.apache.spark.sql.catalyst.analysis.Analyzer.executeAndCheck(Analyzer.scala:103)
at
org.apache.spark.sql.execution.QueryExecution.analyzed$lzycompute(QueryExecution.scala:57)
at
org.apache.spark.sql.execution.QueryExecution.analyzed(QueryExecution.scala:55)
at
org.apache.spark.sql.execution.QueryExecution.assertAnalyzed(QueryExecution.scala:47)
at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:74) at
org.apache.spark.sql.SparkSession.table(SparkSession.scala:627) at
org.apache.spark.sql.SparkSession.table(SparkSession.scala:623) at
org.apache.spark.sql.DataFrameReader.table(DataFrameReader.scala:654) ... 49
elided
{noformat}
Unfortunately, we don't control the creation of table. What would be a config
that could help me read this table?
> NullPointerException on zero-size ORC file
> ------------------------------------------
>
> Key: SPARK-19809
> URL: https://issues.apache.org/jira/browse/SPARK-19809
> Project: Spark
> Issue Type: Bug
> Components: SQL
> Affects Versions: 1.6.3, 2.0.2, 2.1.1, 2.2.1
> Reporter: Michał Dawid
> Assignee: Dongjoon Hyun
> Priority: Major
> Fix For: 2.3.0
>
> Attachments: image-2018-02-26-20-29-49-410.png,
> spark.sql.hive.convertMetastoreOrc.txt
>
>
> When reading from hive ORC table if there are some 0 byte files we get
> NullPointerException:
> {code}java.lang.NullPointerException
> at
> org.apache.hadoop.hive.ql.io.orc.OrcInputFormat$BISplitStrategy.getSplits(OrcInputFormat.java:560)
> at
> org.apache.hadoop.hive.ql.io.orc.OrcInputFormat.generateSplitsInfo(OrcInputFormat.java:1010)
> at
> org.apache.hadoop.hive.ql.io.orc.OrcInputFormat.getSplits(OrcInputFormat.java:1048)
> at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:199)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:242)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:240)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:240)
> at
> org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:242)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:240)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:240)
> at
> org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:242)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:240)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:240)
> at org.apache.spark.rdd.UnionRDD$$anonfun$1.apply(UnionRDD.scala:66)
> at org.apache.spark.rdd.UnionRDD$$anonfun$1.apply(UnionRDD.scala:66)
> at
> scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
> at
> scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
> at scala.collection.immutable.List.foreach(List.scala:318)
> at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
> at scala.collection.AbstractTraversable.map(Traversable.scala:105)
> at org.apache.spark.rdd.UnionRDD.getPartitions(UnionRDD.scala:66)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:242)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:240)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:240)
> at
> org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:242)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:240)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:240)
> at
> org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:190)
> at
> org.apache.spark.sql.execution.Limit.executeCollect(basicOperators.scala:165)
> at
> org.apache.spark.sql.execution.SparkPlan.executeCollectPublic(SparkPlan.scala:174)
> at
> org.apache.spark.sql.DataFrame$$anonfun$org$apache$spark$sql$DataFrame$$execute$1$1.apply(DataFrame.scala:1499)
> at
> org.apache.spark.sql.DataFrame$$anonfun$org$apache$spark$sql$DataFrame$$execute$1$1.apply(DataFrame.scala:1499)
> at
> org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:56)
> at
> org.apache.spark.sql.DataFrame.withNewExecutionId(DataFrame.scala:2086)
> at
> org.apache.spark.sql.DataFrame.org$apache$spark$sql$DataFrame$$execute$1(DataFrame.scala:1498)
> at
> org.apache.spark.sql.DataFrame.org$apache$spark$sql$DataFrame$$collect(DataFrame.scala:1505)
> at
> org.apache.spark.sql.DataFrame$$anonfun$head$1.apply(DataFrame.scala:1375)
> at
> org.apache.spark.sql.DataFrame$$anonfun$head$1.apply(DataFrame.scala:1374)
> at org.apache.spark.sql.DataFrame.withCallback(DataFrame.scala:2099)
> at org.apache.spark.sql.DataFrame.head(DataFrame.scala:1374)
> at org.apache.spark.sql.DataFrame.take(DataFrame.scala:1456)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:497)
> at
> org.apache.zeppelin.spark.ZeppelinContext.showDF(ZeppelinContext.java:209)
> at
> org.apache.zeppelin.spark.SparkSqlInterpreter.interpret(SparkSqlInterpreter.java:129)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.interpret(LazyOpenInterpreter.java:94)
> at
> org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:341)
> at org.apache.zeppelin.scheduler.Job.run(Job.java:176)
> at
> org.apache.zeppelin.scheduler.FIFOScheduler$1.run(FIFOScheduler.java:139)
> at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
> 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:745){code}
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