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From Xiangrui Meng <men...@gmail.com>
Subject Re: Reading from .bz2 files with Spark
Date Tue, 13 May 2014 16:08:53 GMT
Which hadoop version did you use? I'm not sure whether Hadoop v2 fixes
the problem you described, but it does contain several fixes to bzip2
format. -Xiangrui

On Wed, May 7, 2014 at 9:19 PM, Andrew Ash <andrew@andrewash.com> wrote:
> Hi all,
>
> Is anyone reading and writing to .bz2 files stored in HDFS from Spark with
> success?
>
>
> I'm finding the following results on a recent commit (756c96 from 24hr ago)
> and CDH 4.4.0:
>
> Works: val r = sc.textFile("/user/aa/myfile.bz2").count
> Doesn't work: val r = sc.textFile("/user/aa/myfile.bz2").map((s:String) =>
> s+"| " ).count
>
> Specifically, I'm getting an exception coming out of the bzip2 libraries
> (see below stacktraces), which is unusual because I'm able to read from that
> file without an issue using the same libraries via Pig.  It was originally
> created from Pig as well.
>
> Digging a little deeper I found this line in the .bz2 decompressor's javadoc
> for CBZip2InputStream:
>
> "Instances of this class are not threadsafe." [source]
>
>
> My current working theory is that Spark has a much higher level of
> parallelism than Pig/Hadoop does and thus I get these wild IndexOutOfBounds
> exceptions much more frequently (as in can't finish a run over a little 2M
> row file) vs hardly at all in other libraries.
>
> The only other reference I could find to the issue was in presto-users, but
> the recommendation to leave .bz2 for .lzo doesn't help if I actually do want
> the higher compression levels of .bz2.
>
>
> Would love to hear if I have some kind of configuration issue or if there's
> a bug in .bz2 that's fixed in later versions of CDH, or generally any other
> thoughts on the issue.
>
>
> Thanks!
> Andrew
>
>
>
> Below are examples of some exceptions I'm getting:
>
> 14/05/07 15:09:49 WARN scheduler.TaskSetManager: Loss was due to
> java.lang.ArrayIndexOutOfBoundsException
> java.lang.ArrayIndexOutOfBoundsException: 65535
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.hbCreateDecodeTables(CBZip2InputStream.java:663)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.createHuffmanDecodingTables(CBZip2InputStream.java:790)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.recvDecodingTables(CBZip2InputStream.java:762)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode(CBZip2InputStream.java:798)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.initBlock(CBZip2InputStream.java:502)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.changeStateToProcessABlock(CBZip2InputStream.java:333)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.read(CBZip2InputStream.java:397)
>         at
> org.apache.hadoop.io.compress.BZip2Codec$BZip2CompressionInputStream.read(BZip2Codec.java:426)
>         at java.io.InputStream.read(InputStream.java:101)
>         at
> org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:209)
>         at org.apache.hadoop.util.LineReader.readLine(LineReader.java:173)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:203)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:43)
>
>
>
>
> java.lang.ArrayIndexOutOfBoundsException: 900000
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode(CBZip2InputStream.java:900)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.initBlock(CBZip2InputStream.java:502)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.changeStateToProcessABlock(CBZip2InputStream.java:333)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.read(CBZip2InputStream.java:397)
>         at
> org.apache.hadoop.io.compress.BZip2Codec$BZip2CompressionInputStream.read(BZip2Codec.java:426)
>         at java.io.InputStream.read(InputStream.java:101)
>         at
> org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:209)
>         at org.apache.hadoop.util.LineReader.readLine(LineReader.java:173)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:203)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:43)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:198)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:181)
>         at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71)
>         at
> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:35)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$class.foreach(Iterator.scala:727)
>         at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
>         at
> org.apache.spark.rdd.RDD.org$apache$spark$rdd$RDD$$countPartition$1(RDD.scala:868)
>
>
>
> java.lang.ArrayIndexOutOfBoundsException: -921878509
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode0(CBZip2InputStream.java:1011)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode(CBZip2InputStream.java:826)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.initBlock(CBZip2InputStream.java:502)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.changeStateToProcessABlock(CBZip2InputStream.java:333)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.read(CBZip2InputStream.java:397)
>         at
> org.apache.hadoop.io.compress.BZip2Codec$BZip2CompressionInputStream.read(BZip2Codec.java:432)
>         at java.io.InputStream.read(InputStream.java:101)
>         at
> org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:209)
>         at org.apache.hadoop.util.LineReader.readLine(LineReader.java:173)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:203)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:43)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:198)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:181)
>         at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71)
>         at
> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:35)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$class.foreach(Iterator.scala:727)
>         at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
>         at
> org.apache.spark.rdd.RDD.org$apache$spark$rdd$RDD$$countPartition$1(RDD.scala:868)
>         at org.apache.spark.rdd.RDD$$anonfun$24.apply(RDD.scala:879)
>         at org.apache.spark.rdd.RDD$$anonfun$24.apply(RDD.scala:879)
>         at org.apache.spark.rdd.RDD$$anonfun$12.apply(RDD.scala:548)
>         at org.apache.spark.rdd.RDD$$anonfun$12.apply(RDD.scala:548)
>
>
>
> java.lang.ArrayIndexOutOfBoundsException: -1321104434
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode0(CBZip2InputStream.java:1011)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.getAndMoveToFrontDecode(CBZip2InputStream.java:826)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.initBlock(CBZip2InputStream.java:502)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.changeStateToProcessABlock(CBZip2InputStream.java:333)
>         at
> org.apache.hadoop.io.compress.bzip2.CBZip2InputStream.read(CBZip2InputStream.java:397)
>         at
> org.apache.hadoop.io.compress.BZip2Codec$BZip2CompressionInputStream.read(BZip2Codec.java:426)
>         at java.io.InputStream.read(InputStream.java:101)
>         at
> org.apache.hadoop.util.LineReader.readDefaultLine(LineReader.java:209)
>         at org.apache.hadoop.util.LineReader.readLine(LineReader.java:173)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:203)
>         at
> org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:43)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:198)
>         at
> org.apache.spark.rdd.HadoopRDD$$anon$1.getNext(HadoopRDD.scala:181)
>         at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71)
>         at
> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:35)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>         at scala.collection.Iterator$class.foreach(Iterator.scala:727)
>         at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
>         at
> org.apache.spark.rdd.RDD.org$apache$spark$rdd$RDD$$countPartition$1(RDD.scala:868)

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