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From "Hairong Kuang (JIRA)" <j...@apache.org>
Subject [jira] Commented: (HADOOP-1489) Input file get truncated for text files with \r\n
Date Thu, 14 Jun 2007 20:44:27 GMT

    [ https://issues.apache.org/jira/browse/HADOOP-1489?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#action_12504908
] 

Hairong Kuang commented on HADOOP-1489:
---------------------------------------

This is a good one and very subtle too.

The problem is caused by using an external buffer for checksum verification. So FSInputChecker
requires the amount of data read should be at least bytesPerCheccksum, which makes sure that
no checksum verified data are read.

We use Java's BufferedInputStream to implement the external buffer and guranteens that the
buffer size is at least bytePerChecksum. However, in order to support mark() in BufferedInputStream,
BufferedInputStream sometimes may expand its buffer size and issue read that asks for bytes
which are less than bytesPerChecksum. Therefore, we get the problem described in this jira.

The proposal in HADOOP-1470 is to verify checksum using an internal buffer.  So the buffer
size restriction will no longer be required.  Hence a patch to HADOOP-1470 will also resolve
this issue.

An alternative quick fix is to overide markSupported() in FSDataInputStream.Buffer so that
it returns false.



> Input file get truncated for text files with \r\n
> -------------------------------------------------
>
>                 Key: HADOOP-1489
>                 URL: https://issues.apache.org/jira/browse/HADOOP-1489
>             Project: Hadoop
>          Issue Type: Bug
>          Components: io
>    Affects Versions: 0.13.0
>            Reporter: Bwolen Yang
>         Attachments: MRIdentity.java, slashr33.txt
>
>
> When input file has \r\n, LineRecordReader uses mark()/reset() to read one byte ahead
to check if \r is followed by \n.   This probably caused the BufferedInputStream to issue
a small read request (e.g., 127 bytes).   The  ChecksumFileSystem.FSInputChecker.read() code

> {code}
>    public int read(byte b[], int off, int len) throws IOException {
>      // make sure that it ends at a checksum boundary
>      long curPos = getPos();
>      long endPos = len+curPos/bytesPerSum*bytesPerSum;
>      return readBuffer(b, off, (int)(endPos-curPos));
>    }
> {code}
> tries to truncate "len" to checksum boundary.  For DFS, bytesPerSum is 512.  So for small
reads, the truncated length become negative (i.e., endPos - curPos is < 0).   The underlying
DFS read returns 0 when length is negative.  However, readBuffer changes it to -1 assuming
end-of-file has been reached.   This means effectively, the rest of the input file did not
get read.  In my case, only 8MB of a 52MB file is actually read.   Two sample stacks are appended.
> One related issue, if there are assumptions (such as len >= bytesPerSum) in FSInputChecker's
read(), would it be ok to add a check that throws an exception when the assumption is violated?
  This assumption is a bit unusal and as code changes (both Hadoop and Java's implementation
of BufferedInputStream), the assumption may get violated.  This silently dropping large part
of input seems really difficult for people to notice (and debug) when people start to deal
with terabytes of data.   Also, I suspect the performance impact for such a check would not
be noticed.
> bwolen
> Here are two sample stacks.  (i have readbuffer throw when it gets 0 bytes, and have
inputchecker catches the exception and rethrow both.  This way, I catch the values from both
caller and callee (see the callee one starts with "Caused by")
> -------------------------------------
> {code}
> java.lang.RuntimeException: end of read()
> in=org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker len=127
> pos=45223932 res=-999999
>        at org.apache.hadoop.fs.FSDataInputStream$PositionCache.read(FSDataInputStream.java:50)
>        at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
>        at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
>        at org.apache.hadoop.fs.FSDataInputStream$Buffer.read(FSDataInputStream.java:116)
>        at java.io.FilterInputStream.read(FilterInputStream.java:66)
>        at org.apache.hadoop.mapred.LineRecordReader.readLine(LineRecordReader.java:132)
>        at org.apache.hadoop.mapred.LineRecordReader.readLine(LineRecordReader.java:124)
>        at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:108)
>        at org.apache.hadoop.mapred.MapTask$1.next(MapTask.java:168)
>        at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:44)
>        at org.apache.hadoop.mapred.MapTask.run(MapTask.java:186)
>        at org.apache.hadoop.mapred.TaskTracker$Child.main(TaskTracker.java:1720)
> Caused by: java.lang.RuntimeException: end of read()
> datas=org.apache.hadoop.dfs.DFSClient$DFSDataInputStream pos=45223932
> len=-381 bytesPerSum=512 eof=false read=0
>        at org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker.readBuffer(ChecksumFileSystem.java:200)
>        at org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker.read(ChecksumFileSystem.java:175)
>        at org.apache.hadoop.fs.FSDataInputStream$PositionCache.read(FSDataInputStream.java:47)
>        ... 11 more
> ---------------
> java.lang.RuntimeException: end of read()  in=org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker
len=400 pos=4503 res=-999999
> 	at org.apache.hadoop.fs.FSDataInputStream$PositionCache.read(FSDataInputStream.java:50)
> 	at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
> 	at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
> 	at org.apache.hadoop.fs.FSDataInputStream$Buffer.read(FSDataInputStream.java:116)
> 	at java.io.FilterInputStream.read(FilterInputStream.java:66)
> 	at org.apache.hadoop.mapred.LineRecordReader.readLine(LineRecordReader.java:132)
> 	at org.apache.hadoop.mapred.LineRecordReader.readLine(LineRecordReader.java:124)
> 	at org.apache.hadoop.mapred.LineRecordReader.next(LineRecordReader.java:108)
> 	at org.apache.hadoop.mapred.MapTask$1.next(MapTask.java:168)
> 	at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:44)
> 	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:186)
> 	at org.apache.hadoop.mapred.TaskTracker$Child.main(TaskTracker.java:1720)
> Caused by: java.lang.RuntimeException: end of read()  datas=org.apache.hadoop.dfs.DFSClient$DFSDataInputStream
pos=4503 len=-7 bytesPerSum=512 eof=false read=0
> 	at org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker.readBuffer(ChecksumFileSystem.java:200)
> 	at org.apache.hadoop.fs.ChecksumFileSystem$FSInputChecker.read(ChecksumFileSystem.java:175)
> 	at org.apache.hadoop.fs.FSDataInputStream$PositionCache.read(FSDataInputStream.java:47)
> 	... 11 more
> {code}

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