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From Xiangrui Meng <men...@gmail.com>
Subject Re: Reading from .bz2 files with Spark
Date Sat, 17 May 2014 01:48:20 GMT
Hi Andrew,

This is the JIRA I created:
https://issues.apache.org/jira/browse/MAPREDUCE-5893 . Hopefully
someone wants to work on it.

Best,
Xiangrui

On Fri, May 16, 2014 at 6:47 PM, Xiangrui Meng <mengxr@gmail.com> wrote:
> Hi Andre,
>
> I could reproduce the bug with Hadoop 2.2.0. Some older version of
> Hadoop do not support splittable compression, so you ended up with
> sequential reads. It is easy to reproduce the bug with the following
> setup:
>
> 1) Workers are configured with multiple cores.
> 2) BZip2 files are big enough or minPartitions is large enough when
> you load the file via sc.textFile(), so that one worker has more than
> one tasks.
>
> Best,
> Xiangrui
>
> On Fri, May 16, 2014 at 4:06 PM, Andrew Ash <andrew@andrewash.com> wrote:
>> 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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