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From Andrew Ash <and...@andrewash.com>
Subject Re: Reading from .bz2 files with Spark
Date Fri, 16 May 2014 23:06:07 GMT
Hi Xiangrui,

// FYI I'm getting your emails late due to the Apache mailing list outage

I'm using CDH4.4.0, which I think uses the MapReduce v2 API.  The .jars are
named like this: hadoop-hdfs-2.0.0-cdh4.4.0.jar

I'm also glad you were able to reproduce!  Please paste a link to the
Hadoop bug you file so I can follow along.

Thanks!
Andrew


On Tue, May 13, 2014 at 9:08 AM, Xiangrui Meng <mengxr@gmail.com> wrote:

> 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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