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MapReduce, mail # user - Sqoop 1.4.1-cdh4.0.1 is not running in Hadoop 2.0.0-cdh4.1.1


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Sqoop 1.4.1-cdh4.0.1 is not running in Hadoop 2.0.0-cdh4.1.1
Kartashov, Andy 2012-10-23, 19:17
Guys tried for hours to resolve this error.

I am trying to import a table to Hadoop using Sqoop.

ERROR is:
Error: org.hsqldb.DatabaseURL.parseURL(Ljava/lang/String;ZZ)Lorg/hsqldb/persist/HsqlProperties
I realise that there is an issue with the versions of hsqldb.jar files

At first, Sqoop was spitting above error until I realised that my /usr/lib/sqoop/lib folder had both versions hsqldb-1.8.0.10.jar and just hsqldb.jar (2.0? I suppose), and sqoop-conf was picking up the first (wrong jar).

When I moved the hsqldb-1.8.0.10.jar away, Sqoop stopped complaining but them Hadoop began spitting out the same error. No matter what I tried I could not get Hadoop to pick the right jar.

I tried setting:
export HADOOP_CLASSPATH="/usr/lib/sqoop/lib/hsqldb.jar" and then
export HADOOP_USER_CLASSPATH_FIRST=true
without luck..

Please help.

Thnks
AK
From: Jonathan Bishop [mailto:[EMAIL PROTECTED]]
Sent: Tuesday, October 23, 2012 2:41 PM
To: [EMAIL PROTECTED]
Subject: Re: zlib does not uncompress gzip during MR run

Just to follow up on my own question...

I believe the problem is caused by the input split during MR. So my real question is how to handle input splits when the input is gzipped.

Is it even possible to have splits of a gzipped file?

Thanks,

Jon
On Tue, Oct 23, 2012 at 11:10 AM, Jonathan Bishop <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> wrote:
Hi,

My input files are gzipped, and I am using the builtin java codecs successfully to uncompress them in a normal java run...

        fileIn = fs.open(fsplit.getPath());
        codec = compressionCodecs.getCodec(fsplit.getPath());
        in = new LineReader(codec != null ? codec.createInputStream(fileIn) : fileIn, config);

But when I use the same piece of code in a MR job I am getting...
12/10/23 11:02:25 INFO util.NativeCodeLoader: Loaded the native-hadoop library
12/10/23 11:02:25 INFO zlib.ZlibFactory: Successfully loaded & initialized native-zlib library
12/10/23 11:02:25 INFO compress.CodecPool: Got brand-new compressor
12/10/23 11:02:26 INFO mapreduce.HFileOutputFormat: Incremental table output configured.
12/10/23 11:02:26 INFO input.FileInputFormat: Total input paths to process : 3
12/10/23 11:02:27 INFO mapred.JobClient: Running job: job_201210221549_0014
12/10/23 11:02:28 INFO mapred.JobClient:  map 0% reduce 0%
12/10/23 11:02:49 INFO mapred.JobClient: Task Id : attempt_201210221549_0014_m_000003_0, Status : FAILED
java.io.IOException: incorrect header check
    at org.apache.hadoop.io.compress.zlib.ZlibDecompressor.inflateBytesDirect(Native Method)
    at org.apache.hadoop.io.compress.zlib.ZlibDecompressor.decompress(ZlibDecompressor.java:221)
    at org.apache.hadoop.io.compress.DecompressorStream.decompress(DecompressorStream.java:82)
    at org.apache.hadoop.io.compress.DecompressorStream.read(DecompressorStream.java:76)
    at java.io.InputStream.read(InputStream.java:101)
So I am thinking that there is some incompatibility of zlib and my gzip. Is there a way to force hadoop to use the java built-in compression codecs?

Also, I would like to try lzo which I hope will allow splitting of the input files (I recall reading this somewhere). Can someone point me to the best way to do this?

Thanks,

Jon

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