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From Sriram Ramachandrasekaran <sri.ram...@gmail.com>
Subject Re: Deserialization issue.
Date Mon, 30 Jul 2012 13:58:32 GMT
Harsh,
I was waiting to try it on my cluster before I came back to report if it
worked or not.
I tried it and it works. The site wide configuration worked.
The IOUtils.conf.addResource("job.xml") does the same thing as
GoraMapReduceUtils.setIOSerialization(), so it did not help.

Thanks for the help. I still would like to know, what would be a better way
to debug distributed map reduce jobs.
I know I can debug stand-alone jobs quite easily, but, I would like to know
how folks do distributed map reduce jobs debugging.

Thanks again!
-Sriram


On Sat, Jul 28, 2012 at 6:20 AM, Sriram Ramachandrasekaran <
sri.rams85@gmail.com> wrote:

> aah! I always thought about setting io.serializations at the job level. I
> never thought about this. will try this site wide thing. thanks again.
> On 28 Jul 2012 06:16, "Harsh J" <harsh@cloudera.com> wrote:
>
>> Ah, that may be cause the core-site.xml has the property
>> io.serializations fully defined for Gora as well? You can do that as
>> an alternative fix, supply a core-site.xml across tasktrackers that
>> also carry the serialization class Gora requires. I failed to think of
>> that as a solution.
>>
>> On Sat, Jul 28, 2012 at 6:04 AM, Sriram Ramachandrasekaran
>> <sri.rams85@gmail.com> wrote:
>> > okay. But this issue didn't present itself when run in standalone mode.
>> :)
>> >
>> > On 28 Jul 2012 06:02, "Harsh J" <harsh@cloudera.com> wrote:
>> >>
>> >> I find it easier to run jobs via MRUnit (http://mrunit.apache.org,
>> >> TDD) first, or via LocalJobRunner, for debug purposes.
>> >>
>> >> On Sat, Jul 28, 2012 at 5:53 AM, Sriram Ramachandrasekaran
>> >> <sri.rams85@gmail.com> wrote:
>> >> > hello harsh,
>> >> > thanks for your investigations. while we were debugging, I saw the
>> exact
>> >> > thing. As you pointed out, we suspected it to be a problem. So, we
>> set
>> >> > the
>> >> > job conf object directly on Gora's query object.
>> >> > It goes something like this,
>> >> > query.setConf..(job.getConfig..())
>> >> >
>> >> > And, then I saw that it was not getting into creating a new object
at
>> >> > getOrCreate().
>> >> >
>> >> > OTOH, i've not tried the job.xml thing. I should give it a try n I
>> shall
>> >> > keep the loop posted.
>> >> >
>> >> > I would also like to hear about standard practices for debugging
>> >> > distributed
>> >> > MR tasks.
>> >> >
>> >> > -----
>> >> > reply from a hh device. Pl excuse typos n lack of formatting.
>> >> >
>> >> > On 28 Jul 2012 03:30, "Harsh J" <harsh@cloudera.com> wrote:
>> >> >>
>> >> >> Hi Sriram,
>> >> >>
>> >> >> I suspect the following in Gora to somehow be causing this issue:
>> >> >>
>> >> >> IOUtils source:
>> >> >>
>> >> >>
>> >> >>
>> http://svn.apache.org/viewvc/gora/trunk/gora-core/src/main/java/org/apache/gora/util/IOUtils.java?view=markup
>> >> >> QueryBase source:
>> >> >>
>> >> >>
>> >> >>
>> http://svn.apache.org/viewvc/gora/trunk/gora-core/src/main/java/org/apache/gora/query/impl/QueryBase.java?view=markup
>> >> >>
>> >> >> Notice that IOUtils.deserialize(…) calls expect a proper
>> Configuration
>> >> >> object. If not passed (i.e., if null), they call the following.
>> >> >>
>> >> >> 68        private static Configuration getOrCreateConf(Configuration
>> >> >> conf)
>> >> >> {
>> >> >> 69          if(conf == null) {
>> >> >> 70            if(IOUtils.conf == null) {
>> >> >> 71              IOUtils.conf = new Configuration();
>> >> >> 72            }
>> >> >> 73          }
>> >> >> 74          return conf != null ? conf : IOUtils.conf;
>> >> >> 75        }
>> >> >>
>> >> >> Now QueryBase, has in its readFields method, some
>> >> >> IOUtils.deserialize(…) calls, that seem to pass a null for the
>> >> >> configuration object. The IOUtils.deserialize(…) method hence
calls
>> >> >> this above method, and initializes a whole new Configuration object,
>> >> >> as the passed conf object is null.
>> >> >>
>> >> >> If it does that, it would not be loading the "job.xml" file
>> contents,
>> >> >> which is the job's config file (thats something the map task's
>> config
>> >> >> set alone loads, and not a file thats loaded by default). So hence,
>> >> >> custom serializers will disappear the moment it begins using this
>> new
>> >> >> Configuration object.
>> >> >>
>> >> >> This is what you'll want to investigate and fix or notify the Gora
>> >> >> devs about (why QueryBase#readFields uses a null object, and if
it
>> can
>> >> >> reuse some set conf object). As a cheap hack fix, maybe doing the
>> >> >> following will make it work in an MR environment?
>> >> >>
>> >> >> IOUtils.conf = new Configuration();
>> >> >> IOUtils.conf.addResource("job.xml");
>> >> >>
>> >> >> I haven't tried the above, but let us know how we can be of further
>> >> >> assistance. An ideal fix would be to only use the MapTask's provided
>> >> >> Configuration object everywhere, somehow, and never re-create one.
>> >> >>
>> >> >> P.s. If you want a thread ref link to share with other devs over
>> Gora,
>> >> >> here it is: http://search-hadoop.com/m/BXZA4dTUFC
>> >> >>
>> >> >> On Fri, Jul 27, 2012 at 1:24 PM, Sriram Ramachandrasekaran
>> >> >> <sri.rams85@gmail.com> wrote:
>> >> >> > Hello,
>> >> >> > I have an MR job that talks to HBase. I use Gora to talk to
HBase.
>> >> >> > Gora
>> >> >> > also
>> >> >> > provides couple of classes which can be extended to write
Mappers
>> and
>> >> >> > Reducers, if the mappers need input from an HBase store and
>> Reducers
>> >> >> > need to
>> >> >> > write it out to an HBase store. This is the reason why I use
Gora.
>> >> >> >
>> >> >> > Now, when I run my MR job, I get an exception as below.
>> >> >> > (https://issues.apache.org/jira/browse/HADOOP-3093)
>> >> >> > java.lang.RuntimeException: java.io.IOException:
>> >> >> > java.lang.NullPointerException
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.gora.mapreduce.GoraInputFormat.setConf(GoraInputFormat.java:115)
>> >> >> > at
>> >> >> >
>> >> >> >
>> org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:62)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:117)
>> >> >> > at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:723)
>> >> >> > at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370)
>> >> >> > at org.apache.hadoop.mapred.Child$4.run(Child.java:255)
>> >> >> > at java.security.AccessController.doPrivileged(Native Method)
>> >> >> > at javax.security.auth.Subject.doAs(Subject.java:415)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1093)
>> >> >> > at org.apache.hadoop.mapred.Child.main(Child.java:249)
>> >> >> > Caused by: java.io.IOException: java.lang.NullPointerException
>> >> >> > at org.apache.gora.util.IOUtils.loadFromConf(IOUtils.java:483)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.gora.mapreduce.GoraInputFormat.getQuery(GoraInputFormat.java:125)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.gora.mapreduce.GoraInputFormat.setConf(GoraInputFormat.java:112)
>> >> >> > ... 9 more
>> >> >> > Caused by: java.lang.NullPointerException
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.io.serializer.SerializationFactory.getDeserializer(SerializationFactory.java:77)
>> >> >> > at org.apache.gora.util.IOUtils.deserialize(IOUtils.java:205)
>> >> >> > at
>> >> >> >
>> org.apache.gora.query.impl.QueryBase.readFields(QueryBase.java:234)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:67)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:40)
>> >> >> > at
>> >> >> >
>> >> >> >
>> >> >> >
>> org.apache.hadoop.io.DefaultStringifier.fromString(DefaultStringifier.java:75)
>> >> >> > at
>> >> >> >
>> >> >> >
>> org.apache.hadoop.io.DefaultStringifier.load(DefaultStringifier.java:133)
>> >> >> > at org.apache.gora.util.IOUtils.loadFromConf(IOUtils.java:480)
>> >> >> > ... 11 more
>> >> >> >
>> >> >> > I tried the following things to work through this issue.
>> >> >> > 0. The stack trace indicates that, when setting up a new Mapper,
>> it
>> >> >> > is
>> >> >> > unable to deserialize something. (I could not get to understand
>> where
>> >> >> > it
>> >> >> > fails).
>> >> >> > 1. I looked around the forums and realized that serialization
>> options
>> >> >> > are
>> >> >> > not getting passed, so, I tried setting up, io.serializations
>> config
>> >> >> > on
>> >> >> > the
>> >> >> > job.
>> >> >> >    1.1. I am not setting up the "io.serializations" myself,
I use
>> >> >> > GoraMapReduceUtils.setIOSerializations() to do it. I verified
>> that,
>> >> >> > the
>> >> >> > confs are getting proper serializers.
>> >> >> > 2. I verified in the job xml to see if these confs have got
>> through,
>> >> >> > they
>> >> >> > were. But, it failed again.
>> >> >> > 3. I tried starting the hadoop job runner with debug options
>> turned
>> >> >> > on
>> >> >> > and
>> >> >> > in suspend mode, -XDebug suspend=y and I also set the VM options
>> for
>> >> >> > mapred
>> >> >> > child tasks, via the mapred.child.java.opts to see if I can
debug
>> the
>> >> >> > VM
>> >> >> > that gets spawned newly. Although I get a message on my stdout
>> >> >> > saying,
>> >> >> > opening port X and waiting, when I try to attach a remote
>> debugger on
>> >> >> > that
>> >> >> > port, it does not work.
>> >> >> >
>> >> >> > I understand that, when SerializationFactory tries to deSerialize
>> >> >> > 'something', it does not find an appropriate unmarshaller
and so
>> it
>> >> >> > fails.
>> >> >> > But, I would like to know a way to find that 'something' and
I
>> would
>> >> >> > like to
>> >> >> > get some idea on how (pseudo) distributed MR jobs should be
>> generally
>> >> >> > debugged. I tried searching, did not find anything useful.
>> >> >> >
>> >> >> > Any help/pointers would be greatly useful.
>> >> >> >
>> >> >> > Thanks!
>> >> >> >
>> >> >> > --
>> >> >> > It's just about how deep your longing is!
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Harsh J
>> >>
>> >>
>> >>
>> >> --
>> >> Harsh J
>>
>>
>>
>> --
>> Harsh J
>>
>


-- 
It's just about how deep your longing is!

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