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.ram...@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" <ha...@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.ram...@gmail.com> wrote: >> > okay. But this issue didn't present itself when run in standalone mode. >> :) >> > >> > On 28 Jul 2012 06:02, "Harsh J" <ha...@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.ram...@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" <ha...@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.ram...@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!
