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" <[email protected]> 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 > <[email protected]> wrote: > > okay. But this issue didn't present itself when run in standalone mode. > :) > > > > On 28 Jul 2012 06:02, "Harsh J" <[email protected]> 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 > >> <[email protected]> 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" <[email protected]> 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 > >> >> <[email protected]> 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 >
