[jira] [Commented] (SPARK-11177) sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero bytes
[
https://issues.apache.org/jira/browse/SPARK-11177?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=14965007#comment-14965007
]
Steve Loughran commented on SPARK-11177:
0-byte files are a troublespot in object stores, as they are often used/abused
in hadoop fs clients to mimic directories.
One thing to consider is actually skipping 0-byte files on the basis they have
no relevant data whatsoever
> sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero
> bytes
> ---
>
> Key: SPARK-11177
> URL: https://issues.apache.org/jira/browse/SPARK-11177
> Project: Spark
> Issue Type: Sub-task
> Components: Input/Output
>Reporter: Josh Rosen
>Assignee: Josh Rosen
>
> From a user report:
> {quote}
> When I upload a series of text files to an S3 directory and one of the files
> is empty (0 bytes). The sc.wholeTextFiles method stack traces.
> java.lang.ArrayIndexOutOfBoundsException: 0
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat$OneFileInfo.(CombineFileInputFormat.java:506)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getMoreSplits(CombineFileInputFormat.java:285)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getSplits(CombineFileInputFormat.java:245)
> at org.apache.spark.rdd.WholeTextFileRDD.getPartitions(NewHadoopRDD.scala:303)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1922)
> at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:905)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
> at org.apache.spark.rdd.RDD.withScope(RDD.scala:306)
> at org.apache.spark.rdd.RDD.collect(RDD.scala:904)
> {quote}
> It looks like this has been a longstanding issue:
> *
> http://apache-spark-user-list.1001560.n3.nabble.com/pyspark-wholeTextFiles-error-td8872.html
> *
> https://stackoverflow.com/questions/31051107/read-multiple-files-from-a-directory-using-spark
> *
> https://forums.databricks.com/questions/1799/arrayindexoutofboundsexception-with-wholetextfiles.html
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[jira] [Commented] (SPARK-11177) sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero bytes
[
https://issues.apache.org/jira/browse/SPARK-11177?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=14962913#comment-14962913
]
Josh Rosen commented on SPARK-11177:
It looks like this is caused by MAPREDUCE-4470, which is not patched in Apache
Hadoop 1.x releases. If Spark users cannot upgrade to Hadoop 2.x and absolutely
need a fix for this, then one somewhat hacky solution is to use a modified copy
of CombineFileInputFormat which lives in the Spark source tree and includes the
three-line fix for MAPREDUCE-4470. While this works (I have tests!), it's not
an approach which is suitable for inclusion in a Spark release: it's going to
be borderline impossible to maintain source- and binary-compatibility with all
of our supported Hadoop versions while using this approach.
> sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero
> bytes
> ---
>
> Key: SPARK-11177
> URL: https://issues.apache.org/jira/browse/SPARK-11177
> Project: Spark
> Issue Type: Sub-task
>Reporter: Josh Rosen
>Assignee: Josh Rosen
>
> From a user report:
> {quote}
> When I upload a series of text files to an S3 directory and one of the files
> is empty (0 bytes). The sc.wholeTextFiles method stack traces.
> java.lang.ArrayIndexOutOfBoundsException: 0
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat$OneFileInfo.(CombineFileInputFormat.java:506)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getMoreSplits(CombineFileInputFormat.java:285)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getSplits(CombineFileInputFormat.java:245)
> at org.apache.spark.rdd.WholeTextFileRDD.getPartitions(NewHadoopRDD.scala:303)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1922)
> at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:905)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
> at org.apache.spark.rdd.RDD.withScope(RDD.scala:306)
> at org.apache.spark.rdd.RDD.collect(RDD.scala:904)
> {quote}
> It looks like this has been a longstanding issue:
> *
> http://apache-spark-user-list.1001560.n3.nabble.com/pyspark-wholeTextFiles-error-td8872.html
> *
> https://stackoverflow.com/questions/31051107/read-multiple-files-from-a-directory-using-spark
> *
> https://forums.databricks.com/questions/1799/arrayindexoutofboundsexception-with-wholetextfiles.html
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[jira] [Commented] (SPARK-11177) sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero bytes
[
https://issues.apache.org/jira/browse/SPARK-11177?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=14962821#comment-14962821
]
Josh Rosen commented on SPARK-11177:
Reproduced it. This only occurs on Hadoop 1.x.
> sc.wholeTextFiles throws ArrayIndexOutOfBoundsException when S3 file has zero
> bytes
> ---
>
> Key: SPARK-11177
> URL: https://issues.apache.org/jira/browse/SPARK-11177
> Project: Spark
> Issue Type: Sub-task
>Reporter: Josh Rosen
>
> From a user report:
> {quote}
> When I upload a series of text files to an S3 directory and one of the files
> is empty (0 bytes). The sc.wholeTextFiles method stack traces.
> java.lang.ArrayIndexOutOfBoundsException: 0
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat$OneFileInfo.(CombineFileInputFormat.java:506)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getMoreSplits(CombineFileInputFormat.java:285)
> at
> org.apache.hadoop.mapreduce.lib.input.CombineFileInputFormat.getSplits(CombineFileInputFormat.java:245)
> at org.apache.spark.rdd.WholeTextFileRDD.getPartitions(NewHadoopRDD.scala:303)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
> at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
> at scala.Option.getOrElse(Option.scala:120)
> at org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1922)
> at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:905)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
> at org.apache.spark.rdd.RDD.withScope(RDD.scala:306)
> at org.apache.spark.rdd.RDD.collect(RDD.scala:904)
> {quote}
> It looks like this has been a longstanding issue:
> *
> http://apache-spark-user-list.1001560.n3.nabble.com/pyspark-wholeTextFiles-error-td8872.html
> *
> https://stackoverflow.com/questions/31051107/read-multiple-files-from-a-directory-using-spark
> *
> https://forums.databricks.com/questions/1799/arrayindexoutofboundsexception-with-wholetextfiles.html
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